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Sample records for bottlenecks population differentiation

  1. Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii

    DEFF Research Database (Denmark)

    Barker, J.S.F.; Frydenberg, Jane; González, J.

    2009-01-01

    Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from...... that of the original population simply due to genetic drift. Disentangling the effects of founder drift and selection after colonization is crucial to understanding the adaptive process. Drosophila buzzatii colonized Australia some 600-700 generations ago, and spread rapidly over a wide geographical range. Genetic...... through a moderate bottleneck (approximately 30-40 founders). Linkage disequilibrium was common, both intrachromosomal and between loci on different chromosomes. Of the 15 loci, 2 showed evidence of selection, one exhibiting local adaptation in different populations and the other balancing selection. We...

  2. The Impact of Population Bottlenecks on Microbial Adaptation

    Science.gov (United States)

    LeClair, Joshua S.; Wahl, Lindi M.

    2017-11-01

    Population bottlenecks—sudden, severe reductions in population size—are ubiquitous in nature. Because of their critical implications for conservation genetics, the effects of population bottlenecks on the loss of genetic diversity have been well studied. Bottlenecks also have important implications for adaptation, however, and these effects have been addressed more recently, typically in microbial populations. In this short review, we survey both experimental and theoretical work describing the impact of population bottlenecks on microbial adaptation. Focusing on theoretical contributions, we highlight emerging insights and conclude with several open questions of interest in the field.

  3. Host population bottlenecks drive parasite extinction during antagonistic coevolution.

    Science.gov (United States)

    Hesse, Elze; Buckling, Angus

    2016-01-01

    Host-parasite interactions are often characterized by large fluctuations in host population size, and we investigated how such host bottlenecks affected coevolution between a bacterium and a virus. Previous theory suggests that host bottlenecks should provide parasites with an evolutionary advantage, but instead we found that phages were rapidly driven to extinction when coevolving with hosts exposed to large genetic bottlenecks. This was caused by the stochastic loss of sensitive bacteria, which are required for phage persistence and infectivity evolution. Our findings emphasize the importance of feedbacks between ecological and coevolutionary dynamics, and how this feedback can qualitatively alter coevolutionary dynamics. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  4. Evidence for population bottlenecks and subtle genetic structure in the yellow rail

    Science.gov (United States)

    Popper, Kenneth J.; Miller, Leonard F.; Green, Michael; Haig, Susan M.; Mullins, Thomas D.

    2012-01-01

    The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

  5. Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican Parrot

    Science.gov (United States)

    S.R. Beissinger; Jr Wunderle; J.M. Meyers; B.E. Saether; S. Engen

    2008-01-01

    The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk...

  6. The effect of an extreme and prolonged population bottleneck on patterns of deleterious variation

    DEFF Research Database (Denmark)

    Pedersen, Casper-Emil Tingskov; Lohmueller, Kirk E.; Grarup, Niels

    2017-01-01

    more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect......The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly...... that the Inuit have a significantly higher load (20% increase or more) compared to other less bottlenecked human populations. Forward simulations under realistic models of demography support our empirical findings, showing up to a 6% increase in the genetic load for the Inuit population across all models...

  7. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N

    2008-01-01

    According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the trait, bottlenecks may...... effects were responsible for the divergence in desiccation resistance between the original control and a bottlenecked line exhibiting increased additive genetic variance for desiccation resistance. However, when bottlenecked lines were selected for increased desiccation resistance, there was only a small...... actually increase additive genetic variance. This has been an important issue in conservation genetics where it has been suggested that small population size might actually experience an increase rather than a decrease in the rate of adaptation. Here we test if bottlenecks can break a selection limit...

  8. Genome-wide signatures of population bottlenecks and diversifying selection in European wolves.

    Science.gov (United States)

    Pilot, M; Greco, C; vonHoldt, B M; Jędrzejewska, B; Randi, E; Jędrzejewski, W; Sidorovich, V E; Ostrander, E A; Wayne, R K

    2014-04-01

    Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.

  9. Evaluating ring-tailed lemurs (Lemur catta) from southwestern Madagascar for a genetic population bottleneck.

    Science.gov (United States)

    Parga, Joyce A; Sauther, Michelle L; Cuozzo, Frank P; Jacky, Ibrahim Antho Youssouf; Lawler, Richard R

    2012-01-01

    In light of historical and recent anthropogenic influences on Malagasy primate populations, in this study ring-tailed lemur (Lemur catta) samples from two sites in southwestern Madagascar, Beza Mahafaly Special Reserve (BMSR) and Tsimanampetsotsa National Park (TNP), were evaluated for the genetic signature of a population bottleneck. A total of 45 individuals (20 from BMSR and 25 from TNP) were genotyped at seven microsatellite loci. Three methods were used to evaluate these populations for evidence of a historical bottleneck: M-ratio, mode-shift, and heterozygosity excess tests. Three mutation models were used for heterozygosity excess tests: the stepwise mutation model (SMM), two-phase model (TPM), and infinite allele model (IAM). M-ratio estimations indicated a potential bottleneck in both populations under some conditions. Although mode-shift tests did not strongly indicate a population bottleneck in the recent historical past when samples from all individuals were included, a female-only analysis indicated a potential bottleneck in TNP. Heterozygosity excess was indicated under two of the three mutation models (IAM and TPM), with TNP showing stronger evidence of heterozygosity excess than BMSR. Taken together, these results suggest that a bottleneck may have occurred among L. catta in southwestern Madagascar in the recent past. Given knowledge of how current major stochastic climatic events and human-induced change can negatively impact extant lemur populations, it is reasonable that comparable events in the historical past could have caused a population bottleneck. This evaluation additionally functions to highlight the continuing environmental and anthropogenic challenges faced by lemurs in southwestern Madagascar. Copyright © 2011 Wiley Periodicals, Inc.

  10. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.

    Directory of Open Access Journals (Sweden)

    Daniel J Balick

    2015-08-01

    Full Text Available Population bottlenecks followed by re-expansions have been common throughout history of many populations. The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics. On the basis of theoretical analysis and computer simulations, we suggest that this response qualitatively depends on dominance. The number of dominant or additive deleterious alleles per haploid genome is expected to be slightly increased following the bottleneck and re-expansion. In contrast, the number of completely or partially recessive alleles should be sharply reduced. Changes of population size expose differences between recessive and additive selection, potentially providing insight into the prevalence of dominance in natural populations. Specifically, we use a simple statistic, [Formula: see text], where xi represents the derived allele frequency, to compare the number of mutations in different populations, and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. We also provide empirical evidence showing that gene sets associated with autosomal recessive disease in humans may have a BR indicative of recessive selection. Together, these theoretical predictions and empirical observations show that complex demographic history may facilitate rather than impede inference of parameters of natural selection.

  11. On the prospect of identifying adaptive loci in recently bottlenecked populations.

    Directory of Open Access Journals (Sweden)

    Yu-Ping Poh

    Full Text Available Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.

  12. Low genetic diversity in the bottlenecked population of endangered non-native banteng in northern Australia.

    Science.gov (United States)

    Bradshaw, Corey J A; Isagi, Yuji; Kaneko, Shingo; Brook, Barry W; Bowman, David M J S; Frankham, Richard

    2007-07-01

    Undomesticated (wild) banteng are endangered in their native habitats in Southeast Asia. A potential conservation resource for the species is a large, wild population in Garig Gunak Barlu National Park in northern Australia, descended from 20 individuals that were released from a failed British outpost in 1849. Because of the founding bottleneck, we determined the level of genetic diversity in four subpopulations in the national park using 12 microsatellite loci, and compared this to the genetic diversity of domesticated Asian Bali cattle, wild banteng and other cattle species. We also compared the loss of genetic diversity using plausible genetic data coupled to a stochastic Leslie matrix model constructed from existing demographic data. The 53 Australian banteng sampled had average microsatellite heterozygosity (HE) of 28% compared to 67% for outbred Bos taurus and domesticated Bos javanicus populations. The Australian banteng inbreeding coefficient (F) of 0.58 is high compared to other endangered artiodactyl populations. The 95% confidence bounds for measured heterozygosity overlapped with those predicted from our stochastic Leslie matrix population model. Collectively, these results show that Australian banteng have suffered a loss of genetic diversity and are highly inbred because of the initial population bottleneck and subsequent small population sizes. We conclude that the Australian population is an important hedge against the complete loss of wild banteng, and it can augment threatened populations of banteng in their native range. This study indicates the genetic value of small populations of endangered artiodactyls established ex situ.

  13. Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican parrot

    Science.gov (United States)

    Beissenger, S.R.; Wunderle, J.M.; Meyers, J.M.; Saether, B.-E.; Engen, S.

    2008-01-01

    The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 6 5.2 parrots per year, or an average k?1.05 6 0.19) from 16 parrots (1973) to a high of 40-42 birds (1997-1998). A risk analysis based on population prediction intervals (PPI) indicates great risk and large uncertainty, with a range of 22?83 birds in the 90% PPI only five years into the future. Four primary factors (reduced hatching success due to inbreeding, failure of adults to nest, nest failure due to nongenetic causes, and reduced survival of adults and juveniles) were responsible for maintaining the bottleneck. Egghatchability rates were low (70.6% per egg and 76.8% per pair), and hatchability increased after mate changes, suggesting inbreeding effects. Only an average of 34% of the population nested annually, which was well below the percentage of adults that should have reached an age of first breeding (41-56%). This chronic failure to nest appears to have been caused primarily by environmental and/or behavioral factors, and not by nest-site scarcity or a skewed sex ratio. Nest failure rates from nongenetic causes (i.e., predation, parasitism, and wet cavities) were low (29%) due to active management (protecting nests and fostering

  14. The Evopopbot Chip: Ultra High-throughput Evolutionary Population Bottlenecking using Drop-Based Microfluidics

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    Chang, Connie; Rotem, Assaf; Serohijos, Adrian; Zhang, Huidan; Tao, Ye; Fischer Hesselbrock, Audrey; Thielen, Peter; Mehoke, Thomas; Wolfe, Joshua; Wobus, Christiane; Feldman, Andrew; Shakhnovich, Eugene; Weitz, David

    2014-03-01

    The study of how viruses propagate is important for curing disease and preventing viral outbreaks. In nature, viruses can compete with one another, and the most evolutionary fit virus usually takes over a population. Yet there exist variants in the population that can escape subjected evolutionary pressures and eventually dominate the population. Successful studies of viral epidemics hinges on the ability to access these variants. Here, we present the use of droplet-based microfluidics as a simple method to segregate and propagate a viral population as individual viral lineages, simultaneously performing millions of in vitroevolutionary bottlenecking experiments. We introduce a novel microfluidic device, called the ``Evopopbot Chip'', that allows for simultaneous passaging of millions of evolutionary bottlenecking events by splitting drops containing previous generations of viruses and merging with drops containing new host cells. After several generations of viral replication in the evolution chip, we discover hundreds of new viruses that are able to escape a neutralizing antibody selection pressure compared to bulk passaging.

  15. Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization.

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    Baptiste Monsion

    2008-10-01

    Full Text Available The effective size of populations (Ne determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Despite their high mutation rate and rapid evolution, this parameter is poorly documented experimentally in viruses, particularly plant viruses. All available studies, however, have demonstrated the existence of huge within-host demographic fluctuations, drastically reducing Ne upon systemic invasion of different organs and tissues. Notably, extreme bottlenecks have been detected at the stage of systemic leaf colonization in all plant viral species investigated so far, sustaining the general idea that some unknown obstacle(s imposes a barrier on the development of all plant viruses. This idea has important implications, as it appoints genetic drift as a constant major force in plant virus evolution. By co-inoculating several genetic variants of Cauliflower mosaic virus into a large number of replicate host plants, and by monitoring their relative frequency within the viral population over the course of the host systemic infection, only minute stochastic variations were detected. This allowed the estimation of the CaMV Ne during colonization of successive leaves at several hundreds of viral genomes, a value about 100-fold higher than that reported for any other plant virus investigated so far, and indicated the very limited role played by genetic drift during plant systemic infection by this virus. These results suggest that the barriers that generate bottlenecks in some plant virus species might well not exist, or can be surmounted by other viruses, implying that severe bottlenecks during host colonization do not necessarily apply to all plant-infecting viruses.

  16. Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization.

    Science.gov (United States)

    Monsion, Baptiste; Froissart, Rémy; Michalakis, Yannis; Blanc, Stéphane

    2008-10-01

    The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Despite their high mutation rate and rapid evolution, this parameter is poorly documented experimentally in viruses, particularly plant viruses. All available studies, however, have demonstrated the existence of huge within-host demographic fluctuations, drastically reducing Ne upon systemic invasion of different organs and tissues. Notably, extreme bottlenecks have been detected at the stage of systemic leaf colonization in all plant viral species investigated so far, sustaining the general idea that some unknown obstacle(s) imposes a barrier on the development of all plant viruses. This idea has important implications, as it appoints genetic drift as a constant major force in plant virus evolution. By co-inoculating several genetic variants of Cauliflower mosaic virus into a large number of replicate host plants, and by monitoring their relative frequency within the viral population over the course of the host systemic infection, only minute stochastic variations were detected. This allowed the estimation of the CaMV Ne during colonization of successive leaves at several hundreds of viral genomes, a value about 100-fold higher than that reported for any other plant virus investigated so far, and indicated the very limited role played by genetic drift during plant systemic infection by this virus. These results suggest that the barriers that generate bottlenecks in some plant virus species might well not exist, or can be surmounted by other viruses, implying that severe bottlenecks during host colonization do not necessarily apply to all plant-infecting viruses.

  17. Host-Pathogen Checkpoints and Population Bottlenecks in Persistent and Intracellular Uropathogenic E. coli Bladder Infection

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    Hannan, Thomas J.; Totsika, Makrina; Mansfield, Kylie J.; Moore, Kate H.; Schembri, Mark A.; Hultgren, Scott J.

    2013-01-01

    Bladder infections affect millions of people yearly, and recurrent symptomatic infections (cystitis) are very common. The rapid increase in infections caused by multi-drug resistant uropathogens threatens to make recurrent cystitis an increasingly troubling public health concern. Uropathogenic E. coli (UPEC) cause the vast majority of bladder infections. Upon entry into the lower urinary tract, UPEC face obstacles to colonization that constitute population bottlenecks, reducing diversity and selecting for fit clones. A critical mucosal barrier to bladder infection is the epithelium (urothelium). UPEC bypass this barrier when they invade urothelial cells and form intracellular bacterial communities (IBCs), a process which requires type 1 pili. IBCs are transient in nature, occurring primarily during acute infection. Chronic bladder infection is common and can be either latent, in the form of the Quiescent Intracellular Reservoir (QIR), or active, in the form of asymptomatic bacteriuria (ASB/ABU) or chronic cystitis. In mice, the fate of bladder infection: QIR, ASB, or chronic cystitis, is determined within the first 24 hours of infection and constitutes a putative host-pathogen mucosal checkpoint that contributes to susceptibility to recurrent cystitis. Knowledge of these checkpoints and bottlenecks is critical for our understanding of bladder infection and efforts to devise novel therapeutic strategies. PMID:22404313

  18. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant.

    Science.gov (United States)

    Vilà, Carles; Sundqvist, Anna-Karin; Flagstad, Øystein; Seddon, Jennifer; Björnerfeldt, Susanne; Kojola, Ilpo; Casulli, Adriano; Sand, Håkan; Wabakken, Petter; Ellegren, Hans

    2003-01-07

    The fragmentation of populations is an increasingly important problem in the conservation of endangered species. Under these conditions, rare migration events may have important effects for the rescue of small and inbred populations. However, the relevance of such migration events to genetically depauperate natural populations is not supported by empirical data. We show here that the genetic diversity of the severely bottlenecked and geographically isolated Scandinavian population of grey wolves (Canis lupus), founded by only two individuals, was recovered by the arrival of a single immigrant. Before the arrival of this immigrant, for several generations the population comprised only a single breeding pack, necessarily involving matings between close relatives and resulting in a subsequent decline in individual heterozygosity. With the arrival of just a single immigrant, there is evidence of increased heterozygosity, significant outbreeding (inbreeding avoidance), a rapid spread of new alleles and exponential population growth. Our results imply that even rare interpopulation migration can lead to the rescue and recovery of isolated and endangered natural populations.

  19. Bottlenecks and multiple introductions: Population genetics of the vector of avian malaria in Hawaii

    Science.gov (United States)

    Fonseca, Dina M.; LaPointe, Dennis A.; Fleischer, Robert C.

    2000-01-01

    Avian malaria has had a profound impact on the demographics and behaviour of Hawaiian forest birds since its vector, Culex quinquefasciatusthe southern house mosquito, was first introduced to Hawaii around 1830. In order to understand the dynamics of the disease in Hawaii and gain insights into the evolution of vector-mediated parasite–host interactions in general we studied the population genetics of Cx. quinquefasciatus in the Hawaiian Islands. We used both microsatellite and mitochondrial loci. Not surprisingly we found that mosquitoes in Midway, a small island in the Western group, are quite distinct from the populations in the main Hawaiian Islands. However, we also found that in general mosquito populations are relatively isolated even among the main islands, in particular between Hawaii (the Big Island) and the remaining Hawaiian Islands. We found evidence of bottlenecks among populations within the Big Island and an excess of alleles in Maui, the site of the original introduction. The mitochondrial diversity was typically low but higher than expected. The current distribution of mitochondrial haplotypes combined with the microsatellite information lead us to conclude that there have been several introductions and to speculate on some processes that may be responsible for the current population genetics of vectors of avian malaria in Hawaii.

  20. Population bottleneck triggering millennial-scale morphospace shifts in endemic thermal-spring melanopsids.

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    Neubauer, Thomas A; Harzhauser, Mathias; Georgopoulou, Elisavet; Wrozyna, Claudia

    2014-11-15

    For more than hundred years the thermal spring-fed Lake Pețea near Oradea, Romania, was studied for its highly endemic subfossil and recent fauna and flora. One point of focus was the species lineage of the melanopsid gastropod Microcolpia parreyssii , which exhibited a tremendous diversity of shapes during the earlier Holocene. As a consequence many new species, subspecies, and variety-names have been introduced over time, trying to categorize this overwhelming variability. In contrast to the varied subfossil assemblage, only a single phenotype is present today. We critically review the apparent "speciation event" implied by the taxonomy, based on the presently available information and new data from morphometric analyses of shell outlines and oxygen and carbon isotope data. This synthesis shows that one turning point in morphological evolution coincides with high accumulation of peaty deposits during a short time interval of maximally a few thousand years. The formation of a small, highly eutrophic swamp with increased input of organic matter marginalized the melanopsids and reduced population size. The presented data make natural selection as the dominating force unlikely but rather indicates genetic drift following a bottleneck effect induced by the environmental changes. This claim contrasts the "obvious trend" and shows that great morphological variability has to be carefully and objectively evaluated in order to allow sound interpretations of the underlying mechanisms.

  1. Population genetics and the effects of a severe bottleneck in an ex situ population of critically endangered Hawaiian tree snails.

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    Price, Melissa R; Hadfield, Michael G

    2014-01-01

    As wild populations decline, ex situ propagation provides a potential bank of genetic diversity and a hedge against extinction. These programs are unlikely to succeed if captive populations do not recover from the severe bottleneck imposed when they are founded with a limited number of individuals from remnant populations. In small captive populations allelic richness may be lost due to genetic drift, leading to a decline in fitness. Wild populations of the Hawaiian tree snail Achatinella lila, a hermaphroditic snail with a long life history, have declined precipitously due to introduced predators and other human impacts. A captive population initially thrived after its founding with seven snails, exceeding 600 captive individuals in 2009, but drastically declined in the last five years. Measures of fitness were examined from 2,018 captive snails that died between 1998 and 2012, and compared with genotypic data for six microsatellite loci from a subset of these deceased snails (N = 335), as well as live captive snails (N = 198) and wild snails (N = 92). Surprisingly, the inbreeding coefficient (Fis) declined over time in the captive population, and is now approaching values observed in the 2013 wild population, despite a significant decrease in allelic richness. However, adult annual survival and fecundity significantly declined in the second generation. These measures of fitness were positively correlated with heterozygosity. Snails with higher measures of heterozygosity had more offspring, and third generation offspring with higher measures of heterozygosity were more likely to reach maturity. These results highlight the importance of maintaining genetic diversity in captive populations, particularly those initiated with a small number of individuals from wild remnant populations. Genetic rescue may allow for an increase in genetic diversity in the captive population, as measures of heterozygosity and rarified allelic richness were higher in wild tree

  2. Population aging and migrant workers: bottlenecks in tuberculosis control in rural China.

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    Bele, Sumedh; Jiang, Wei; Lu, Hui; You, Hua; Fan, Hong; Huang, Lifang; Wang, Qungang; Shen, Hongbing; Wang, Jianming

    2014-01-01

    Tuberculosis is a serious global health problem. Its paradigms are shifting through time, especially in rapidly developing countries such as China. Health providers in China are at the forefront of the battle against tuberculosis; however, there are few empirical studies on health providers' perspectives on the challenges they face in tuberculosis control at the county level in China. This study was conducted among health providers to explore their experiences with tuberculosis control in order to identify bottlenecks and emerging challenges in controlling tuberculosis in rural China. A qualitative approach was used. Semi-structured, in-depth interviews were conducted with 17 health providers working in various positions within the health system of one rural county (ZJG) of China. Data were analyzed based on thematic content analysis using MAXQDA 10 qualitative data analysis software. Health providers reported several problems in tuberculosis control in ZJG county. Migrant workers and the elderly were repeatedly documented as the main obstacles in effective tuberculosis control in the county. At a personal level, doctors showed their frustration with the lack of new drugs for treating tuberculosis patients, and their opinions varied regarding incentives for referring patients. The results suggest that several problems still remain for controlling tuberculosis in rural China. Tuberculosis control efforts need to make reaching the most vulnerable populations a priority and encourage local health providers to adopt innovative practices in the local context based on national guidelines to achieve the best results. Considerable changes in China's National Tuberculosis Control Program are needed to tackle these emerging challenges faced by health workers at the county level.

  3. Variation at innate immunity Toll-like receptor genes in a bottlenecked population of a New Zealand robin.

    Directory of Open Access Journals (Sweden)

    Catherine E Grueber

    Full Text Available Toll-like receptors (TLRs are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura, for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.

  4. Mechanisms of population differentiation in seabirds.

    Science.gov (United States)

    Friesen, V L; Burg, T M; McCoy, K D

    2007-05-01

    Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain

  5. Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

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    Johannes A. Lenstra

    2014-03-01

    Full Text Available Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

  6. Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri).

    Science.gov (United States)

    Emami-Khoyi, Arsalan; Paterson, Adrian M; Hartley, David A; Boren, Laura J; Cruickshank, Robert H; Ross, James G; Murphy, Elaine C; Else, Terry-Ann

    2017-05-25

    The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.

  7. Logistics bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-09-15

    Many of the vulnerabilities to Energy Access, Energy Security, and Environmental Sustainability result from impediments to reaching a global demand-supply balance, as well as local balances, for various energy sources and carriers. Vulnerabilities result from multiple reasons: regional imbalances of energy production and consumption, the bulky character of the majority of energy fuels, the virtual necessity of electricity consumption following its production, among others. To detect and prioritize respective 'bottlenecks' across energy carriers, they have to be measured. In this report, production, consumption, exports, and imports were measured across all major energy carriers for seven key regions of the world for three time frames-2008, 2020, and 2050. Imbalances between production and consumption form bottlenecks in each region.

  8. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  9. Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum

    Science.gov (United States)

    Moura, Andre E.; Janse van Rensburg, Charlene; Pilot, Malgorzata; Tehrani, Arman; Best, Peter B.; Thornton, Meredith; Plön, Stephanie; de Bruyn, P.J. Nico; Worley, Kim C.; Gibbs, Richard A.; Dahlheim, Marilyn E.; Hoelzel, Alan Rus

    2014-01-01

    Ecosystem function and resilience is determined by the interactions and independent contributions of individual species. Apex predators play a disproportionately determinant role through their influence and dependence on the dynamics of prey species. Their demographic fluctuations are thus likely to reflect changes in their respective ecological communities and habitat. Here, we investigate the historical population dynamics of the killer whale based on draft nuclear genome data for the Northern Hemisphere and mtDNA data worldwide. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. Global mtDNA data indicate that while most populations declined, at least one population retained diversity in a stable, productive ecosystem off southern Africa. We conclude that environmental changes during the last glacial period promoted the decline of a top ocean predator, that these events contributed to the pattern of diversity among extant populations, and that the relatively high diversity of a population currently in productive, stable habitat off South Africa suggests a role for ocean productivity in the widespread decline. PMID:24497033

  10. Meta-Analysis of mitochondrial DNA reveals several population bottlenecks during worldwide migrations of cattle

    NARCIS (Netherlands)

    Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Beja-Pereira, Albano; Bollongino, Ruth; Bradley, Daniel G.; Colli, Licia; De Gaetano, Anna; Edwards, Ceiridwen J.; Felius, Marleen; Ferretti, Luca; Ginja, Catarina; Hristov, Peter; Kantanen, Juha; Lirón, Juan Pedro; Magee, David A.; Negrini, Riccardo; Radoslavov, Georgi A.

    2014-01-01

    Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle

  11. Maintenance of Genetic Diversity in an Introduced Island Population of Guanacos after Seven Decades and Two Severe Demographic Bottlenecks: Implications for Camelid Conservation

    Science.gov (United States)

    von Borries, Rainer; Johnson, Warren E.; Franklin, William L.; Marín, Juan C.

    2014-01-01

    Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10–20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation. PMID:24663026

  12. Maintenance of genetic diversity in an introduced island population of guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation.

    Directory of Open Access Journals (Sweden)

    Benito A González

    Full Text Available Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10-20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego, but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.

  13. Genetic differentiation in geographically close populations of the water rat Nectomys squamipes (Rodentia, Sigmodontinae from the Brazilian Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Maroja L.S.

    2003-01-01

    Full Text Available We examined the genetic structure and the effects of a bottleneck in populations of the water rat Nectomys squamipes, a primary host of Schistosoma mansoni. Eight microsatellite loci were studied in 7 populations from the Sumidouro region of the Brazilian state of Rio de Janeiro. Our data, covering a four-year period during which a bottleneck occurred, revealed substantial variation (6-31 alleles per locus and high levels of both observed (0.718-0.789 and expected (0.748-0.832 heterozygosity. Most populations were in Hardy-Weinberg equilibrium without linkage disequilibrium between loci. Overall average genetic differentiation between populations (estimated with the F ST (q and R ST (r analogues was 0.037 for q and 0.060 for r. There was significant allelic and genotypic differentiation between populations, especially in pairwise comparisons that included the most geographically isolated population. Direct migration estimates showed a low rate of migration, indicating that infected N. squamipes populations had a limited ability to spread S. mansoni. When the pre- and post-bottleneck populations were compared there was no detectable reduction in heterozygosity or allele number, although a significant excess of heterozygosity was detected in the post-bottleneck population.

  14. Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source-sink metapopulation structure, founder events and population bottlenecks.

    Science.gov (United States)

    Barson, N J; Cable, J; Van Oosterhout, C

    2009-03-01

    Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation-drift equilibrium. Dominant downstream migration over both short- and long-time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source-sink metapopulation, with the tributary furthest downstream representing a 'super sink', receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.

  15. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis).

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J; Robertson, Bruce C

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  16. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis.

    Directory of Open Access Journals (Sweden)

    Nicolas Dussex

    Full Text Available The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis. Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410, historical (n = 15 and fossil samples (n = 4 showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  17. Patterns of differentiation among endangered pondberry populations

    Science.gov (United States)

    Craig S Echt; Dennis Deemer; Danny Gustafson

    2011-01-01

    Pondberry, Lindera melissifolia, is an endangered and partially clonally reproducing shrub species found in isolated populations that inhabit seasonally wet depressions in forested areas of the lower Mississippi River alluvial valley and southeastern regions of the United States. With eleven microsatellite loci, we quantified population genetic differentiation and...

  18. Genetic differentiation between natural and hatchery populations of Manila clam (Ruditapes philippinarum) based on microsatellite markers.

    Science.gov (United States)

    Xing, K; Gao, M L; Li, H J

    2014-01-17

    Manila clam (Ruditapes philippinarum) is one of the major aquaculture species around the world and supports an important segment of the aquaculture industry in China. In this study, we used ten microsatellite markers to detect genetic diversity within six R. philippinarum populations and genetic differentiation between them. A total of 109 alleles were detected across all loci. Compared to wild populations (N(A) = 8.4-9.1 alleles/locus, H(E) = 0.75-0.77, H(O) = 0.67-0.73), hatchery stocks showed less genetic variation as revealed in lower number of alleles and lower heterozygosity (N(A) = 7.4-7.5 alleles/locus, H(E) = 0.72-0.75, H(O) = 0.68-0.70), indicating that a bottleneck effect has occurred in hatchery history. Significant genetic differentiation was observed between cultured stocks (P hatchery practices for the preservation of genetic diversity in wild populations.

  19. Traffic behavior at freeway bottlenecks.

    Science.gov (United States)

    2014-09-01

    This study examines traffic behavior in the vicinity of a freeway bottleneck, revisiting commonly held : assumptions and uncovering systematic biases that likely have distorted empirical studies of bottleneck : formation, capacity drop, and the funda...

  20. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Si-Fa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  1. High and distinct range-edge genetic diversity despite local bottlenecks.

    Directory of Open Access Journals (Sweden)

    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  2. Where do they come from? Flow connectivity detects landscape bottlenecks

    Directory of Open Access Journals (Sweden)

    Alessandro Ferrarini

    2015-03-01

    Full Text Available In this paper, bottleneck flow connectivity is first introduced. A landscape bottleneck is defined here as the portion of an arbitrary study area which inevitably tunnels a specimen towards the point where it has been detected in situ. In other words, a bottleneck delimits the portion of the study area which forces the specimen to pass through the detected point of presence with, at most, a tolerance distance equal to an a priori defined uncertainty. There is one precise reason for the introduction of bottleneck flow connectivity: when a specimen is detected through in situ observations or GPS devices, it should be possible to derive the portion of the landscape where it can come from. In fact, the detected specimen is usually just one individual of an entire population that is moving somewhere in the landscape. Hence, such specimen can work as a tracker of the whole population if we have the proper methodological tools to turn its detected position into a map where the landscape bottleneck of the detected location is delineated. In case of a species of conservation interest, the application of bottleneck flow connectivity is useful for the individuation and then the conservation of such population. In case of an exotic undesired species, bottleneck flow connectivity can help individuate the location of the population that should be eradicated, starting from few field observations. An applicative example for wolf in the Ceno Valley (Italy is provided. Bottleneck flow connectivity has thus interesting implications both for the conservation of species of interest, but also for the management of undesired exotic species.

  3. Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae Endemic to Southwest China by Multiple Molecular Markers

    Directory of Open Access Journals (Sweden)

    Xiuyan Feng

    2017-05-01

    Full Text Available Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs, three nuclear genes (nDNAs and 12 nuclear microsatellites (SSRs, we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida.

  4. Bayesian analysis of genetic differentiation between populations.

    Science.gov (United States)

    Corander, Jukka; Waldmann, Patrik; Sillanpää, Mikko J

    2003-01-01

    We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.

  5. Bottlenecks to coral recovery in the Seychelles

    Science.gov (United States)

    Chong-Seng, K. M.; Graham, N. A. J.; Pratchett, M. S.

    2014-06-01

    Processes that affect recovery of coral assemblages require investigation because coral reefs are experiencing a diverse array of more frequent disturbances. Potential bottlenecks to coral recovery include limited larval supply, low rates of settlement, and high mortality of new recruits or juvenile corals. We investigated spatial variation in local abundance of scleractinian corals in the Seychelles at three distinct life history stages (recruits, juveniles, and adults) on reefs with differing benthic conditions. Following widespread coral loss due to the 1998 bleaching event, some reefs are recovering (i.e., relatively high scleractinian coral cover: `coral-dominated'), some reefs have low cover of living macrobenthos and unconsolidated rubble substrates (`rubble-dominated'), and some reefs have high cover of macroalgae (`macroalgal-dominated'). Rates of coral recruitment to artificial settlement tiles were similar across all reef conditions, suggesting that larval supply does not explain differential coral recovery across the three reef types. However, acroporid recruits were absent on macroalgal-dominated reefs (0.0 ± 0.0 recruits tile-1) in comparison to coral-dominated reefs (5.2 ± 1.6 recruits tile-1). Juvenile coral colony density was significantly lower on macroalgal-dominated reefs (2.4 ± 1.1 colonies m-2), compared to coral-dominated reefs (16.8 ± 2.4 m-2) and rubble-dominated reefs (33.1 ± 7.3 m-2), suggesting that macroalgal-dominated reefs have either a bottleneck to successful settlement on the natural substrates or a high post-settlement mortality bottleneck. Rubble-dominated reefs had very low cover of adult corals (10.0 ± 1.7 %) compared to coral-dominated reefs (33.4 ± 3.6 %) despite no statistical difference in their juvenile coral densities. A bottleneck caused by low juvenile colony survivorship on unconsolidated rubble-dominated reefs is possible, or alternatively, recruitment to rubble-dominated reefs has only recently begun. This

  6. Evolutionary forces shaping genomic islands of population differentiation in humans

    Directory of Open Access Journals (Sweden)

    Hofer Tamara

    2012-03-01

    Full Text Available Abstract Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM. A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i as much as 20% of islands are in non-genic regions ii these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii most loci are

  7. Strategic behavior and social outcomes in a bottleneck queue

    DEFF Research Database (Denmark)

    Breinbjerg, Jesper Breinbjerg; Sebald, Alexander Christopher; Østerdal, Lars Peter

    2016-01-01

    We theoretically and experimentally study the differential incentive effects of three well known queue disciplines in a strategic environment in which a bottleneck facility opens and impatient players decide when to arrive. For a class of three-player games, we derive equilibrium arrivals under...

  8. A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks

    DEFF Research Database (Denmark)

    Muwanika, Vincent B.; Siegismund, Hans Redlef; Okello, John Bosco A.

    2003-01-01

    varied in the different parks across different animal species. We have investigated the genetic effects of these reductions in four mammalian species (the common warthog, African savannah elephant, savannah buffalo and common river hippopotamus) from the three major parks of Uganda using both...... microsatellite loci (for elephant and warthog populations) and mitochondrial control sequence variation in the warthogs, elephants, buffaloes and hippopotamuses. Queen Elizabeth National Park showed extreme reduction in nucleotide diversity for two species, the common warthog (p= 0.0%) and African elephant (p= 0.......4%); no such decrease was found for the two other species, the buffalo (p= 3.7-5.4%) and hippopotamus (p= 1.7-1.9%), in the three parks. Nuclear microsatellite markers on the other hand showed high gene diversity in all populations in the common warthog (mean He 0.66-0.78) and the African savannah elephant (mean He 0...

  9. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.E.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58_N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of common

  10. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.E.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58°N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of common

  11. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58 degrees N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of

  12. Analysis of microsatellite DNA markers reveals no genetic differentiation between wild and hatchery populations of Pacific threadfin in Hawaii.

    Science.gov (United States)

    Pan, Gang; Yang, Jinzeng

    2010-12-15

    Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS) DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (F(ST)) and analysis of molecular variance (AMOVA) showed no genetic differentiation between the wild and hatchery populations (F(ST) = 0.001, CI(95%) = -0.01-0.021). Both high genetic diversity (H(o) = 0.664-0.674 and H(e) = 0.710-0.715) and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (F(IS) = 0.052-0.072) in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.

  13. Genetic population differentiation and connectivity among fragmented Moor frog (Rana arvalis) populations in The Netherlands

    NARCIS (Netherlands)

    Arens, P.F.P.; Sluis, van der T.; Westende, van 't W.P.C.; Vosman, B.; Vos, C.C.; Smulders, M.J.M.

    2007-01-01

    We studied the effects of landscape structure, habitat loss and fragmentation on genetic differentiation of Moor frog populations in two landscapes in The Netherlands (Drenthe and Noord-Brabant). Microsatellite data of eight loci showed small to moderate genetic differentiation among populations in

  14. Sales bottlenecks and their effect on profit

    NARCIS (Netherlands)

    Veltman, M.; Kooij, R.E.; Marban, S.

    2014-01-01

    This study introduces the term sales bottleneck, defined as a stage in a total production or service delivery process that limits sales. After analyzing the suitability of traditional methods to find sales bottlenecks, the study proposes the bottleneck accounting model as a method to determine sales

  15. Habitat type predicts genetic population differentiation in freshwater invertebrates.

    Science.gov (United States)

    Marten, Andreas; Brändle, Martin; Brandl, Roland

    2006-08-01

    A basic challenge in evolutionary biology is to establish links between ecology and evolution of species. One important link is the habitat template. It has been hypothesized, that the spatial and temporal settings of a habitat strongly influence the evolution of species dispersal propensity. Here, we evaluate the importance of the habitat type on genetic population differentiation of species using freshwater habitats as a model system. Freshwater habitats are either lentic (standing) or lotic (running). On average, lotic habitats are more stable and predictable over space and time than lentic habitats. Therefore, lentic habitats should favour the evolution of higher dispersal propensity which ensures population survival of lentic species. To test for such a relationship, we used extensive data on species' genetic population differentiation of lentic and lotic freshwater invertebrates retrieved from published allozyme studies. Overall, we analysed more than 150 species from all over the world. Controlling for several experimental, biological and geographical confounding effects, we always found that lentic invertebrates exhibit, on average, lower genetic population differentiation than lotic species. This pattern was consistent across insects, crustaceans and molluscs. Our results imply fundamental differences in genetic population differentiation among species adapted to either lentic or lotic habitats. We propose that such differences should occur in a number of other habitat types that differ in spatio-temporal stability. Furthermore, our results highlight the important role of lotic habitats as reservoirs for evolutionary processes and the potential for rapid speciation.

  16. Periodic solutions of nonautonomous differential systems modeling obesity population

    Energy Technology Data Exchange (ETDEWEB)

    Arenas, Abraham J. [Departamento de Matematicas y Estadistica, Universidad de Cordoba Monteria (Colombia)], E-mail: aarenas@sinu.unicordoba.edu.co; Gonzalez-Parra, Gilberto [Departamento de Calculo, Universidad de los Andes, Merida (Venezuela, Bolivarian Republic of)], E-mail: gcarlos@ula.ve; Jodar, Lucas [Instituto de Matematica Multidisciplinar, Universidad Politecnica de Valencia Edificio 8G, 2o, 46022 Valencia (Spain)], E-mail: ljodar@imm.upv.es

    2009-10-30

    In this paper we study the periodic behaviour of the solutions of a nonautonomous model for obesity population. The mathematical model represented by a nonautonomous system of nonlinear ordinary differential equations is used to model the dynamics of obese populations. Numerical simulations suggest periodic behaviour of subpopulations solutions. Sufficient conditions which guarantee the existence of a periodic positive solution are obtained using a continuation theorem based on coincidence degree theory.

  17. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

    Directory of Open Access Journals (Sweden)

    Alicia R Martin

    2014-08-01

    Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

  18. Genetic diversity and bottleneck analysis of Yunnan mithun ( Bos ...

    African Journals Online (AJOL)

    Mithun or gayal (Bos frontalis) is endemic to the Gaoligongshan Mountains and Drung River Basin in Yunnan, China; a rare and endangered Bos species. To evaluate the genetic diversity and bottleneck effect of Yunnan mithun population, we screened 16 bovine microsatellite loci of Yunnan mithun (N = 34) to provide ...

  19. Genetic structure and bottleneck studies at the malate ...

    African Journals Online (AJOL)

    Levene's and Nei's expected heterozygosities were 0.804 + 0.02 and 0.801 + 0.02, respectively. Wright's fixation ... panmictic unit. A normal 'L' shaped distribution of mode-shift test and three heterozygote excess tests suggested that there was no recent bottleneck in the population of neem at the two enzyme gene loci.

  20. Synergy between Allopatry and Ecology in Population Differentiation and Speciation

    Directory of Open Access Journals (Sweden)

    Yann Surget-Groba

    2012-01-01

    Full Text Available The general diversity pattern of the Caribbean anole radiation has been described in detail; however, the actual mechanisms at the origin of their diversification remain controversial. In particular, the role of ecological speciation, and the relative importance of divergence in allopatry and in parapatry, is debated. We describe the genetic structure of anole populations across lineage contact zones and ecotones to investigate the effect of allopatric divergence, natural selection, and the combination of both factors on population differentiation. Allopatric divergence had no significant impact on differentiation across the lineage boundary, while a clear bimodality in genetic and morphological characters was observed across an ecotone within a single lineage. Critically, the strongest differentiation was observed when allopatry and ecology act together, leading to a sharp reduction in gene flow between two lineages inhabiting different habitats. We suggest that, for Caribbean anoles to reach full speciation, a synergistic combination of several historical and ecological factors may be requisite.

  1. Genetic differentiation of populations residing in areas of high ...

    Indian Academy of Sciences (India)

    ... Public Lectures · Lecture Workshops · Refresher Courses · Symposia. Home; Journals; Journal of Genetics; Volume 88; Issue 1. Genetic differentiation of populations residing in areas of high malaria endemicity in India. Swapnil Sinha Vandana Arya Sarita Agarwal Indian Genome Variation Consortium Saman Habib.

  2. Parameter Estimates in Differential Equation Models for Population Growth

    Science.gov (United States)

    Winkel, Brian J.

    2011-01-01

    We estimate the parameters present in several differential equation models of population growth, specifically logistic growth models and two-species competition models. We discuss student-evolved strategies and offer "Mathematica" code for a gradient search approach. We use historical (1930s) data from microbial studies of the Russian biologist,…

  3. Genetic Differentiation in Native and Introduced Populations of Cryptolaemus montrouzieri (Coleoptera: Coccinellidae) and Its Implications for Biological Control Programs.

    Science.gov (United States)

    Li, Hao-Sen; Jin, Meng-Jie; Ślipiński, Adam; De Clercq, Patrick; Pang, Hong

    2015-10-01

    Cryptolaemus montrouzieri Mulsant (Coleoptera: Coccinellidae) is an effective biological control agent of Australian origin, which has been introduced worldwide to control mealybugs. Although successfully used for >100 yr, its introduction in a new area may cause environmental risks should the populations become invasive. In the present study, a population genetics method was used to make predictions of the invasive potential of C. montrouzieri. Our results showed a similar level of genetic diversity among all populations. No significant genetic differentiation between native and introduced populations was observed, while three populations from the native region were significantly divergent. The fact that genetic diversity was not reduced in introduced areas suggests that no bottleneck effect has occurred during introduction. To avoid rapid evolution of the introduced C. montrouzieri, the introduction records of each population should be clearly traced and introductions from multiple sources into the same area should be avoided. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

    2013-01-01

    method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based...... individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage....... on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled...

  5. Analysis of pharmacogenomic variants associated with population differentiation.

    Directory of Open Access Journals (Sweden)

    Bora Yeon

    Full Text Available In the present study, we systematically investigated population differentiation of drug-related (DR genes in order to identify common genetic features underlying population-specific responses to drugs. To do so, we used the International HapMap project release 27 Data and Pharmacogenomics Knowledge Base (PharmGKB database. First, we compared four measures for assessing population differentiation: the chi-square test, the analysis of variance (ANOVA F-test, Fst, and Nearest Shrunken Centroid Method (NSCM. Fst showed high sensitivity with stable specificity among varying sample sizes; thus, we selected Fst for determining population differentiation. Second, we divided DR genes from PharmGKB into two groups based on the degree of population differentiation as assessed by Fst: genes with a high level of differentiation (HD gene group and genes with a low level of differentiation (LD gene group. Last, we conducted a gene ontology (GO analysis and pathway analysis. Using all genes in the human genome as the background, the GO analysis and pathway analysis of the HD genes identified terms related to cell communication. "Cell communication" and "cell-cell signaling" had the lowest Benjamini-Hochberg's q-values (0.0002 and 0.0006, respectively, and "drug binding" was highly enriched (16.51 despite its relatively high q-value (0.0142. Among the 17 genes related to cell communication identified in the HD gene group, five genes (STX4, PPARD, DCK, GRIK4, and DRD3 contained single nucleotide polymorphisms with Fst values greater than 0.5. Specifically, the Fst values for rs10871454, rs6922548, rs3775289, rs1954787, and rs167771 were 0.682, 0.620, 0.573, 0.531, and 0.510, respectively. In the analysis using DR genes as the background, the HD gene group contained six significant terms. Five were related to reproduction, and one was "Wnt signaling pathway," which has been implicated in cancer. Our analysis suggests that the HD gene group from PharmGKB is

  6. Phenotypic divergence despite low genetic differentiation in house sparrow populations.

    Science.gov (United States)

    Ben Cohen, Shachar; Dor, Roi

    2018-01-10

    Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST) was lower in comparison to phenotypic variation (P ST), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.

  7. Post-ice age recolonization and differentiation of Fucus serratus L. (Phaeophyceae; Fucaceae) populations in Northern Europe.

    Science.gov (United States)

    Coyer, J A; Peters, A F; Stam, W T; Olsen, J L

    2003-07-01

    The seaweed Fucus serratus is hypothesized to have evolved in the North Atlantic and present populations are thought to reflect recolonization from a southern refugium since the last glacial maximum 18 000-20 000 years bp. We examined genetic structure across several spatial scales by analysing seven microsatellite loci in populations collected from 21 localities throughout the species' range. Spatial auto-correlation analysis of seven microsatellite loci revealed no evidence for spatial clustering of alleles on a scale of 100 m despite limited gamete dispersal in F. serratus of approximately 2 m from parental individuals. Pairwise theta analysis suggested that the minimal panmictic unit for F. serratus was between 0.5 and 2 km. Isolation by distance was significant along some contiguous coastlines. Population differentiation was strong within the Skagerrak-Kattegat-Baltic Seas (SKB) (global theta= 0.17) despite a short history of approximately 7500 years. A neighbour-joining tree based on Reynold's distances computed from the microsatellite data revealed a central assemblage of populations on the Brittany Peninsula surrounded by four well-supported clusters consisting of the SKB, the North Sea (Ireland, Helgoland), and two populations from the northern Spanish coast. Samples from Iceland and Nova Scotia were most closely aligned with northwest Sweden and Brittany, respectively. When sample sizes were standardized (N = 41), allelic diversity was twofold higher for Brittany populations than for populations to the north and threefold higher than southern populations. The Brittany region may be a refugium or a recolonized area, whereas the Spanish populations most likely reflect present-day edge populations that have undergone repeated bottlenecks as a consequence of thermally induced cycles of recolonization and extinction.

  8. Genomic diversity and differentiation of a managed island wild boar population

    DEFF Research Database (Denmark)

    Iacolina, Laura; Scandura, Massimo; J. Goedbloed, Daniel

    2016-01-01

    .169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small...... ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support...

  9. Geographical structure and differential natural selection among North European populations

    DEFF Research Database (Denmark)

    McEvoy, Brian P; Montgomery, Grant W; McRae, Allan F

    2009-01-01

    reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to the HLA-G gene on chromosome 6. Evidence of the sweep extends over a 8-Mb/3.5-cM region. Overall, the results illustrate the power of dense genotype and sample......Population structure can provide novel insight into the human past, and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP...... from F(ST)-based analysis of genic and nongenic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps...

  10. Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions

    Science.gov (United States)

    Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Seixas, Pedro P.; Courtot, Karen

    2015-01-01

    Conservation of genetic biodiversity in endangered wildlife populations is an important challenge to address since the loss of alleles and genetic drift may influence future adaptability. Reintroduction aims to re-establish species to restored or protected ecosystems; however, moving a subset of individuals may result in loss of gene variants during the management-induced bottleneck (i.e. translocation). The endangered Laysan teal Anas laysanensis was once widespread across the Hawaiian archipelago, but became isolated on Laysan Island (415 ha) from the mid-1800s until 2004 when a translocation to Midway Atoll (596 ha) was undertaken to reduce extinction risks. We compared genetic diversity and quantified variation at microsatellite loci sampled from 230 individuals from the wild populations at Laysan (1999 to 2009) and Midway (2007 to 2010; n = 133 Laysan, n = 96 Midway birds). We identified polymorphic markers by screening nuclear microsatellites (N = 83). Low nuclear variation was detected, consistent with the species’ insular isolation and historical bottleneck. Six of 83 microsatellites were polymorphic. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within populations. However, 2 rare alleles found in the Laysan source population were not present in Midway’s reintroduced population, and a unique allele was discovered in an individual on Midway. Differentiation between island populations was low (FST = 0.6%), but statistically significant. Our results indicate that genetic drift had little effect on offspring generations 3 to 6 yr post-release and demonstrate the utility of using known founder events to help quantify genetic capture during translocations and to inform management decisions.

  11. Analytical approach to continuous and intermittent bottleneck flows

    DEFF Research Database (Denmark)

    Helbing, Dirk; Johansson, Anders; Mathiesen, Joachim

    2006-01-01

    Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20......Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20...

  12. Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.

    Science.gov (United States)

    Sobel Leonard, Ashley; Weissman, Daniel B; Greenbaum, Benjamin; Ghedin, Elodie; Koelle, Katia

    2017-07-15

    The bottleneck governing infectious disease transmission describes the size of the pathogen population transferred from the donor to the recipient host. Accurate quantification of the bottleneck size is particularly important for rapidly evolving pathogens such as influenza virus, as narrow bottlenecks reduce the amount of transferred viral genetic diversity and, thus, may decrease the rate of viral adaptation. Previous studies have estimated bottleneck sizes governing viral transmission by using statistical analyses of variants identified in pathogen sequencing data. These analyses, however, did not account for variant calling thresholds and stochastic viral replication dynamics within recipient hosts. Because these factors can skew bottleneck size estimates, we introduce a new method for inferring bottleneck sizes that accounts for these factors. Through the use of a simulated data set, we first show that our method, based on beta-binomial sampling, accurately recovers transmission bottleneck sizes, whereas other methods fail to do so. We then apply our method to a data set of influenza A virus (IAV) infections for which viral deep-sequencing data from transmission pairs are available. We find that the IAV transmission bottleneck size estimates in this study are highly variable across transmission pairs, while the mean bottleneck size of 196 virions is consistent with a previous estimate for this data set. Furthermore, regression analysis shows a positive association between estimated bottleneck size and donor infection severity, as measured by temperature. These results support findings from experimental transmission studies showing that bottleneck sizes across transmission events can be variable and influenced in part by epidemiological factors. IMPORTANCE The transmission bottleneck size describes the size of the pathogen population transferred from the donor to the recipient host and may affect the rate of pathogen adaptation within host populations. Recent

  13. Population genomics and the causes of local differentiation.

    Science.gov (United States)

    Tonsor, Stephen J

    2012-11-01

    Exactly 50 years ago, a revolution in empirical population genetics began with the introduction of methods for detecting allelic variation using protein electrophoresis (Throckmorton 1962; Hubby 1963; Lewontin & Hubby 1966). These pioneering scientists showed that populations are chock-full of genetic variation. This variation was a surprise that required a re-thinking of evolutionary genetic heuristics. Understanding the causes for the maintenance of this variation became and remains a major area of research. In the process of addressing the causes, this same group of scientists documented geographical genetic structure (Prakash et al. 1969), spawning the continued accumulation of what is now a huge case study catalogue of geographical differentiation (e.g. Loveless & Hamrick 1984; Linhart & Grant 1996). Geographical differentiation is clearly quite common. Yet, a truly general understanding of the patterns in and causes of spatial genetic structure across the genome remains elusive. To what extent is spatial structure driven by drift and phylogeography vs. geographical differences in environmental sources of selection? What proportion of the genome participates? A general understanding requires range-wide data on spatial patterning of variation across the entire genome. In this issue of Molecular Ecology, Lasky et al. (2012) make important strides towards addressing these issues, taking advantage of three contemporary revolutions in evolutionary biology. Two are technological: high-throughput sequencing and burgeoning computational power. One is cultural: open access to data from the community of scientists and especially data sets that result from large collaborative efforts. Together, these developments may at last put answers within reach.

  14. The Simulation Utilization for the Bottleneck Identification

    Directory of Open Access Journals (Sweden)

    Petra Vegnerová

    2009-12-01

    Full Text Available Advancing globalization increasingly leads to the creation of delivery systems. Increasing competition forces companies to reduce costs permanently. Both of these trends lead to the need to control material and information flows precisely. The target of this article is to describe and show one of ways of bottleneck determination in the supply system. This study deals with the computer simulation and its utilization for assessment of bottleneck. The foundation of the work is created a model of the supply system, it is used to compare the costs associated with the existence of stocks and stock levels in the individual partner of the system, depending on the location of the bottleneck. This article is published as a part of the research intention MSM 6046137306.

  15. Hyperbolic partial differential equations populations, reactors, tides and waves theory and applications

    CERN Document Server

    Witten, Matthew

    1983-01-01

    Hyperbolic Partial Differential Equations, Volume 1: Population, Reactors, Tides and Waves: Theory and Applications covers three general areas of hyperbolic partial differential equation applications. These areas include problems related to the McKendrick/Von Foerster population equations, other hyperbolic form equations, and the numerical solution.This text is composed of 15 chapters and begins with surveys of age specific population interactions, populations models of diffusion, nonlinear age dependent population growth with harvesting, local and global stability for the nonlinear renewal eq

  16. Surviving in isolation: genetic variation, bottlenecks and reproductive strategies in the Canarian endemic Limonium macrophyllum (Plumbaginaceae).

    Science.gov (United States)

    Jiménez, Ares; Weigelt, Barbara; Santos-Guerra, Arnoldo; Caujapé-Castells, Juli; Fernández-Palacios, José María; Conti, Elena

    2017-02-01

    Oceanic archipelagos are typically rich in endemic taxa, because they offer ideal conditions for diversification and speciation in isolation. One of the most remarkable evolutionary radiations on the Canary Islands comprises the 16 species included in Limonium subsection Nobiles, all of which are subject to diverse threats, and legally protected. Since many of them are single-island endemics limited to one or a few populations, there exists a risk that a loss of genetic variation might limit their long-term survival. In this study, we used eight newly developed microsatellite markers to characterize the levels of genetic variation and inbreeding in L. macrophyllum, a species endemic to the North-east of Tenerife that belongs to Limonium subsection Nobiles. We detected generally low levels of genetic variation over all populations (H T = 0.363), and substantial differentiation among populations (F ST = 0.188; R ST = 0.186) coupled with a negligible degree of inbreeding (F = 0.042). Obligate outcrossing may have maintained L. macrophyllum relatively unaffected by inbreeding despite the species' limited dispersal ability and the genetic bottlenecks likely caused by a prolonged history of grazing. Although several factors still constitute a risk for the conservation of L. macrophyllum, the lack of inbreeding and the recent positive demographic trends observed in the populations of this species are factors that favour its future persistence.

  17. Bottleneck analysis at district level to illustrate gaps within the district health system in Uganda.

    Science.gov (United States)

    Kiwanuka Henriksson, Dorcus; Fredriksson, Mio; Waiswa, Peter; Selling, Katarina; Swartling Peterson, Stefan

    2017-01-01

    Poor quality of care and access to effective and affordable interventions have been attributed to constraints and bottlenecks within and outside the health system. However, there is limited understanding of health system barriers to utilization and delivery of appropriate, high-impact, and cost-effective interventions at the point of service delivery in districts and sub-districts in low-income countries. In this study we illustrate the use of the bottleneck analysis approach, which could be used to identify bottlenecks in service delivery within the district health system. A modified Tanahashi model with six determinants for effective coverage was used to determine bottlenecks in service provision for maternal and newborn care. The following interventions provided during antenatal care were used as tracer interventions: use of iron and folic acid, intermittent presumptive treatment for malaria, HIV counseling and testing, and syphilis testing. Data from cross-sectional household and health facility surveys in Mayuge and Namayingo districts in Uganda were used in this study. Effective coverage and human resource gaps were identified as the biggest bottlenecks in both districts, with coverage ranging from 0% to 66% for effective coverage and from 46% to 58% for availability of health facility staff. Our findings revealed a similar pattern in bottlenecks in both districts for particular interventions although the districts are functionally independent. The modified Tanahashi model is an analysis tool that can be used to identify bottlenecks to effective coverage within the district health system, for instance, the effective coverage for maternal and newborn care interventions. However, the analysis is highly dependent on the availability of data to populate all six determinants and could benefit from further validation analysis for the causes of bottlenecks identified.

  18. Individual Microscopic Results Of Bottleneck Experiments

    CERN Document Server

    Bukáček, Marek; Krbálek, Milan

    2016-01-01

    This contribution provides microscopic experimental study of pedestrian motion in front of the bottleneck, explains the high variance of individual travel time by the statistical analysis of trajectories. The analysis shows that this heterogeneity increases with increasing occupancy. Some participants were able to reach lower travel time due more efficient path selection and more aggressive behavior within the crowd. Based on this observations, linear model predicting travel time with respect to the aggressiveness of pedestrian is proposed.

  19. Genetic differentiation of populations residing in areas of high ...

    Indian Academy of Sciences (India)

    : rs1800629, rs361525; ICAM-1: rs5491; TLR9: rs187084 and FCGR2A: rs1801274), previously correlated with severity of falciparum malaria in some world popu- lations, was used to analyse genetic differentiation among.

  20. Phenotypic plasticity and population differentiation in an ongoing species invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available The ability to succeed in diverse conditions is a key factor allowing introduced species to successfully invade and spread across new areas. Two non-exclusive factors have been suggested to promote this ability: adaptive phenotypic plasticity of individuals, and the evolution of locally adapted populations in the new range. We investigated these individual and population-level factors in Polygonum cespitosum, an Asian annual that has recently become invasive in northeastern North America. We characterized individual fitness, life-history, and functional plasticity in response to two contrasting glasshouse habitat treatments (full sun/dry soil and understory shade/moist soil in 165 genotypes sampled from nine geographically separate populations representing the range of light and soil moisture conditions the species inhabits in this region. Polygonum cespitosum genotypes from these introduced-range populations expressed broadly similar plasticity patterns. In response to full sun, dry conditions, genotypes from all populations increased photosynthetic rate, water use efficiency, and allocation to root tissues, dramatically increasing reproductive fitness compared to phenotypes expressed in simulated understory shade. Although there were subtle among-population differences in mean trait values as well as in the slope of plastic responses, these population differences did not reflect local adaptation to environmental conditions measured at the population sites of origin. Instead, certain populations expressed higher fitness in both glasshouse habitat treatments. We also compared the introduced-range populations to a single population from the native Asian range, and found that the native population had delayed phenology, limited functional plasticity, and lower fitness in both experimental environments compared with the introduced-range populations. Our results indicate that the future spread of P. cespitosum in its introduced range will likely be

  1. Low population genetic differentiation in the Orchidaceae: implications for the diversification of the family.

    Science.gov (United States)

    Phillips, Ryan D; Dixon, Kingsley W; Peakall, Rod

    2012-11-01

    A leading hypothesis for the immense diversity of the Orchidaceae is that skewed mating success and small, disjunct populations lead to strong genetic drift and switches between adaptive peaks. This mechanism is only possible under conditions of low gene flow that lead to high genetic differentiation among populations. We tested whether orchids typically exhibit high levels of population genetic differentiation by conducting a meta-analysis to compare mean levels of population genetic differentiation (F(ST)) between orchids and other diverse families and between rare and common orchids. Compared with other families, the Orchidaceae is typically characterized by relatively low genetic differentiation among populations (mean F(ST) = 0.146) at allozyme loci. Rare terrestrial orchids showed higher population genetic differentiation than common orchids, although this value was still lower than the mean for most plant families. All lines of evidence suggest that orchids are typically characterized by low levels of population genetic differentiation, even in species with naturally disjunct populations. As such, we found no strong evidence that genetic drift in isolated populations has played a major role in the diversification of the Orchidaceae. Further research into the diversification of the family needs to unravel the relative roles of biotic and environmental selective pressures in the speciation of orchids. © 2012 Blackwell Publishing Ltd.

  2. Population differentiation of Potamogeton pectinatus in the Baltic Sea with reference to waterfowl dispersal.

    Science.gov (United States)

    King, R A; Gornall, R J; Preston, C D; Croft, J M

    2002-10-01

    Forty populations of Potamogeton pectinatus L. were sampled from around the Baltic Sea basin. Analysis of 62 ISSR 'loci' showed that the number of clones per population is very variable but shows a tendency to decrease with latitude. Analysis of molecular variance revealed that, overall, just over half the variability is stored within populations and just under half between them (phi(ST) 0.496). In pairwise comparisons, most populations are significantly differentiated. Genetic distance between populations, as measured by phi(ST), increases with geographical distance. Levels of population differentiation, however, are lower on the southeastern Swedish coast than elsewhere, a reduction correlated with the importance of this area as a staging post for the massive migrations of waterfowl from arctic Russia and western Siberia. Cumulative plots of phi(ST) against geographical distance along this coast suggest that, although it does not prevent significant population differentiation, bird traffic reduces it over distances of 150-200 km.

  3. Plant protein for food: opportunities and bottlenecks

    Directory of Open Access Journals (Sweden)

    Chardigny Jean-Michel

    2016-07-01

    Full Text Available Dietary proteins represent a key issue for the future regarding worldwide food security. Besides animal sources, plant proteins represent an opportunity to mainly contribute to protein demand. Whether some plant protein sources could appear as deficient in some essential amino acids, mixtures from different sources could represent opportunities to further propose adapted supply regarding specific demand. Such opportunities includes legumes as well as by-products of oil processing, i.e. canola and sunflower cakes. The nutritional benefits of such new sources are still under investigation considering benefits and limits like allergenicity. Finally, consumer behavior and acceptability remains the final bottleneck for developing new protein sources.

  4. Evidence for genetic differentiation at the microgeographic scale in Phlebotomus papatasi populations from Sudan.

    Science.gov (United States)

    Khalid, Noteila M; Aboud, Marium A; Alrabba, Fathi M; Elnaiem, Dia-Eldin A; Tripet, Frederic

    2012-11-12

    Cutaneous Leishmaniasis (CL) is endemic in Sudan. It is caused by Leishmania major parasites and transmitted by Phlebotomus papatasi sandflies. Recently, uncommon clinical manifestations of CL have been reported. Moreover, L. donovani parasites that cause Visceral Leishmaniasis (VL) have been isolated from CL lesions of some patients who contracted the disease in Khartoum State, Central Sudan with no history of travelling to VL endemic sites on south-eastern Sudan. Because different clinical manifestations and the parasite behaviour could be related to genetic differentiation, or even sub-structuring within sandfly vector populations, a population genetic study was conducted on P. papatasi populations collected from different localities in Khartoum State known for their uncommon CL cases and characterized by contrasting environmental conditions. A set of seven microsatellite loci was used to investigate the population structure of P. papatasi samples collected from different localities in Khartoum State, Central Sudan. Populations from Kassala State, Eastern Sudan and Egypt were also included in the analyses as outgroups. The level of genetic diversity and genetic differentiation among natural populations of P. papatasi was determined using FST statistics and Bayesian assignments. Genetic analyses revealed significant genetic differentiation (FST) between the Sudanese and the Egyptian populations. Within the Sudanese P. papatasi populations, one population from Gerif West, Khartoum State, exhibited significant genetic differentiation from all other populations including those collected as near as 22 km. The significant genetic differentiation of Gerif West P. papatasi population from other Sudanese populations may have important implication for the epidemiology of leishmaniasis in Khartoum State and needs to be further investigated. Primarily, it could be linked to the unique location of Gerif West which is confined by the River Nile and its tributaries that may

  5. Differential response of two sourgrass populations to glyphosate

    Directory of Open Access Journals (Sweden)

    São Paulo State University, Jaboticabal, SP, Brazil

    2013-02-01

    Full Text Available The repetitive use of glyphosate may cause increase on the resistance of sourgrass (Digitaria insularis through mechanisms of natural selection. The aim of this study was to verify the response of two populations of sourgrass (one collected from nonagricultural area and the other one from area suspected of glyphosate resistance to increasing doses of glyphosate. The experimental design was completely randomized with four repetitions. For both populations, glyphosate was sprayed at 10 doses (0D, D/16, D/8, D/4, D/2, D, 2D, 4D, 8D, and 16D; so that D is the dose of 1.08 kg e.a. ha-1. The treatments were sprayed when the plants had shown 3-5 tillers. The population collected in the nonagricultural area was slightly more sensible to the herbicide glyphosate than the population originated from an area where the herbicide application is common, not indicating glyphosate resistance.

  6. Genetic differentiation, effective population size and gene flow in marine fishes : implications for stock management

    OpenAIRE

    Jose M., CANO; Takahito, Shikano; Anna, KUPARINEN; Juha, MERILA; Ecological Genetics Research Unit, Department of Bio- and Environmental Sciences

    2008-01-01

    Many commercially exploited marine fish and mollusc species exhibit no or a low degree of genetic differentiation in neutral marker genes. This lack of genetic differentiation, typically attributed to high degree of gene flow in marine environments, has sometimes supported the thinking that genetically indistinguishable stocks can be managed as being one panmictic population. Recent comparative studies of neutral marker gene and quantitative trait differentiation in a wide variety of taxa - i...

  7. Genetic diversity and population differentiation of Sclerotinia sclerotiorum collected from canola in China and in USA

    Science.gov (United States)

    Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity wa...

  8. Electronic Bottleneck and Coherent Vibrational Effect on Relaxation Dynamics of Photoexcited Ions in Crystals

    National Research Council Canada - National Science Library

    Alfano, R. R

    2000-01-01

    .... The nonequilibrium population of a local mode of 765 cm(sup -1) in Cr(sup 4+):Mg2SiO4 was found to build up during the transition through an electronic bottleneck and decay by interaction with a restricted number of phonon modes...

  9. Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation

    Directory of Open Access Journals (Sweden)

    Diniz-Filho José Alexandre Felizola

    2000-01-01

    Full Text Available In the present study, we used both simulations and real data set analyses to show that, under stochastic processes of population differentiation, the concepts of spatial heterogeneity and spatial pattern overlap. In these processes, the proportion of variation among and within a population (measured by G ST and 1 - G ST, respectively is correlated with the slope and intercept of a Mantel's test relating genetic and geographic distances. Beyond the conceptual interest, the inspection of the relationship between population heterogeneity and spatial pattern can be used to test departures from stochasticity in the study of population differentiation.

  10. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    KAUST Repository

    Karmin, Monika

    2015-04-30

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

  11. Regional differentiation among populations of the Diamondback terrapin (Malaclemys terrapin)

    Science.gov (United States)

    Hart, Kristen M.; Hunter, Margaret E.; King, Tim L.

    2014-01-01

    The Diamondback terrapin (Malaclemys terrapin) is a brackish-water turtle species whose populations have been fragmented due to anthropogenic activity such as development of coastal habitat and entrapment in commercial blue crab (Callinectes sapidus) fishing gear. Genetic analyses can improve conservation efforts for the long-term protection of the species. We used microsatellite DNA analysis to investigate levels of gene flow among and genetic variability within 21 geographically separate collections of the species distributed from Massachusetts to Texas. Quantified levels of genetic variability (allelic diversity, genotypic frequencies, and heterozygosity) revealed three zones of genetic discontinuity, resulting in four discrete populations: Northeast Atlantic, Coastal Mid-Atlantic, Florida and Texas/Louisiana. The average number of alleles and expected heterozygosity for the four genetic clusters were NA = 6.54 and HE = 0.050, respectively. However, the geographic boundaries of the populations did not correspond to accepted terrapin subspecies limits. Our results illuminate not only the need to sample terrapins in additional sites, specifically in the southeast, but also the necessity for allowing uninterrupted gene flow among population groupings to preserve current levels of genetic diversity.

  12. Multiple Stressor Differential Tolerances: Possible Implications at the Population Level.

    Science.gov (United States)

    Venâncio, Cátia; Ribeiro, Rui; Soares, Amadeu; Lopes, Isabel

    2016-01-01

    The probability of the most sensitive genotypes being eliminated from a population due to a contaminant pulse--genetic erosion--is negatively associated to the within-genotype variation. A sensitive genotype with a small phenotypic variation would be more prone to be lost-a critically sensitive genotype. Furthermore, natural populations inhabiting contaminated sites are usually exposed to several pollutants. Such co- or sequential exposure can have severe effects if at least some tolerant clonal lineages surviving one contaminant are sensitive to the others. Such an inverse relationship coupled with a low within-genotype variation potentially enhances genetic erosion. Accordingly, this study evaluated co-tolerance and the occurrence of clonal lineages critically sensitive to 48-hours lethal exposures of copper, zinc, cobalt, and chromium among eight clonal lineages of the cladocerans Daphnia longispina. Median lethal concentrations (LC50) of each metal were found to have the potential to provoke genetic erosion. Pairwise comparisons of LC50, from the eight clonal lineages, revealed neither negative nor positive correlations (r ≤ |0.56|; p ≥ 0.18), but inversely sensitive clonal lineages were found for all pairs of metals. Therefore, besides having the potential to eliminate critically sensitive clonal lineages in a first intermediately lethal pulse, all tested metals may provoke further losses of clonal lineages in an already genetically eroded population.

  13. Differential stress resistance and metabolic traits underlie coexistence in a sympatrically evolved bacterial population

    NARCIS (Netherlands)

    Puentes Tellez, Pilar; van Elsas, Jan Dirk

    Following intermittent batch growth in Luria-Bertani (LB) broth for about 1000 generations, differentially evolved forms were found in a population of Escherichia coli cells. Studies on this population revealed the emergence of key polymorphisms, as evidenced by analysis of both whole genome

  14. Morphological differentiation of Polygonum viviparum (Polygonaceae in European populations

    Directory of Open Access Journals (Sweden)

    Marcysiak Katarzyna

    2013-12-01

    Full Text Available The variation of Polygonum viviparum L. in Europe was studied in 584 plants sampled from 14 populations at different altitudes and from different substrates in the Carpathians, Alps, Dinaric Alps, Pyrenees and Scandinavian Mts. The samples were analyzed biometrically, using 12 measured stem and inflorescence characters and 10 characters calculated from those 12. The obtained ranges of values were only slightly wider than those given in the literature. All characters significantly differed between populations and six characters were statistically significant in identifying differences between regions. Altitude, substrate and the interactions between them significantly affected the differences in characters between samples. The values of most of the measured characters were lower in samples from higher locations and on poor substrate than in those from lower localities and on rich substrate. Substrate type affected the calculated characters less but it influenced the shift between vegetative and generative reproduction. Multidimensional analyses confirmed the proximity of samples from regions either geographically close or linked via routes of postglacial migrations, despite altitude and substrate differences between them.

  15. Landscape influences on genetic differentiation among bull trout populations in a stream-lake network

    Science.gov (United States)

    Meeuwig, M.H.; Guy, C.S.; Kalinowski, S.T.; Fredenberg, W.A.

    2010-01-01

    This study examined the influence of landscape heterogeneity on genetic differentiation between migratory bull trout (Salvelinus confluentus) populations in Glacier National Park, Montana. An information-theoretic approach was used to compare different conceptual models of dispersal associated with barriers, different models of isolation by distance, and the combined effects of barriers, waterway distance, patch size, and intra- and inter-drainage distribution of populations on genetic differentiation between bull trout populations. The effect of distance between populations on genetic differentiation was best explained by partitioning the effects of mainstem and tributary stream sections. Models that categorized barriers as having a one-way effect (i.e. allowed downstream dispersal) or a two-way effect were best supported. Additionally, patch size and the distribution of populations among drainages influenced genetic differentiation. Genetic differentiation between bull trout populations in Glacier National Park is linked to landscape features that restrict dispersal. However, this analysis illustrates that modelling variability within landscape features, such as dispersal corridors, will benefit landscape genetic analyses. Additionally, the framework used for evaluating the effects of barriers must consider not just barrier presence, but also potential asymmetries in barrier effects with respect to the organism under investigation.

  16. Population genomics of early events in the ecological differentiation of bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Shapiro, Jesse B. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Broad Inst., Cambridge, MA (United States); Friedman, Jonatan [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Cordero, Otto X. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Preheim, Sarah P.. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Timberlake, Sonia C. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Szabo, Gitta [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Polz, Martin F. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Alm, Eric J. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Broad Inst., Cambridge, MA (United States)

    2012-04-06

    Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.

  17. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

    2013-01-01

    Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...... individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage........ In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel...

  18. Evidence of low genetic variation and rare alleles in a bottlenecked endangered island endemic, the Lasan Teal (Anas laysanensis)

    Science.gov (United States)

    Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Peters Jeffrey L,; Courtot, Karen; Seixas, Pedro P.

    2015-01-01

    significant, levels of differentiation (0.6%) between island populations suggesting that genetic drift (as a result of translocation-induced population bottlenecking) has had a limited effect within five years post-release. Our results have utility for informing translocation and genetic management decisions.

  19. Evidence for genetic differentiation at the microgeographic scale in Phlebotomus papatasi populations from Sudan

    Directory of Open Access Journals (Sweden)

    Khalid Noteila M

    2012-11-01

    Full Text Available Abstract Background Cutaneous Leishmaniasis (CL is endemic in Sudan. It is caused by Leishmania major parasites and transmitted by Phlebotomus papatasi sandflies. Recently, uncommon clinical manifestations of CL have been reported. Moreover, L. donovani parasites that cause Visceral Leishmaniasis (VL have been isolated from CL lesions of some patients who contracted the disease in Khartoum State, Central Sudan with no history of travelling to VL endemic sites on south-eastern Sudan. Because different clinical manifestations and the parasite behaviour could be related to genetic differentiation, or even sub-structuring within sandfly vector populations, a population genetic study was conducted on P. papatasi populations collected from different localities in Khartoum State known for their uncommon CL cases and characterized by contrasting environmental conditions. Methods A set of seven microsatellite loci was used to investigate the population structure of P. papatasi samples collected from different localities in Khartoum State, Central Sudan. Populations from Kassala State, Eastern Sudan and Egypt were also included in the analyses as outgroups. The level of genetic diversity and genetic differentiation among natural populations of P. papatasi was determined using FST statistics and Bayesian assignments. Results Genetic analyses revealed significant genetic differentiation (FST between the Sudanese and the Egyptian populations. Within the Sudanese P. papatasi populations, one population from Gerif West, Khartoum State, exhibited significant genetic differentiation from all other populations including those collected as near as 22 km. Conclusion The significant genetic differentiation of Gerif West P. papatasi population from other Sudanese populations may have important implication for the epidemiology of leishmaniasis in Khartoum State and needs to be further investigated. Primarily, it could be linked to the unique location of Gerif West

  20. Rapid differentiation of sexual signals in invasive toads: call variation among populations

    Science.gov (United States)

    Yasumiba, Kiyomi; Duffy, Richard L.; Parsons, Scott A.; Alford, Ross A.; Schwarzkopf, Lin

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls from four populations of different ages since invasion, and analysed the geographic differentiation of seven call parameters. Our comparisons indicate that the calls of R. marina differ among Australian populations. The signal variation was not simply clinal with respect to population age, climate, or morphological differentiation. We suggest that selection on signalling among populations has been idiosyncratic and may reflect local female preferences or adaptation to environmental factors that are not clinal such as energy availability. PMID:27328666

  1. Habitat Fragmentation Differentially Affects Genetic Variation, Phenotypic Plasticity and Survival in Populations of a Gypsum Endemic.

    Science.gov (United States)

    Matesanz, Silvia; Rubio Teso, María Luisa; García-Fernández, Alfredo; Escudero, Adrián

    2017-01-01

    Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia , a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population's similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations' survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness, our study highlights

  2. Deep Complementary Bottleneck Features for Visual Speech Recognition

    NARCIS (Netherlands)

    Petridis, Stavros; Pantic, Maja

    Deep bottleneck features (DBNFs) have been used successfully in the past for acoustic speech recognition from audio. However, research on extracting DBNFs for visual speech recognition is very limited. In this work, we present an approach to extract deep bottleneck visual features based on deep

  3. Epigenetic differentiation persists after male gametogenesis in natural populations of the perennial herb Helleborus foetidus (Ranunculaceae).

    Science.gov (United States)

    Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

    2013-01-01

    Despite the importance of assessing the stability of epigenetic variation in non-model organisms living in real-world scenarios, no studies have been conducted on the transgenerational persistence of epigenetic structure in wild plant populations. This gap in knowledge is hindering progress in the interpretation of natural epigenetic variation. By applying the methylation-sensitive amplified fragment length polymorphism (MSAP) technique to paired plant-pollen (i.e., sporophyte-male gametophyte) DNA samples, and then comparing methylation patterns and epigenetic population differentiation in sporophytes and their descendant gametophytes, we investigated transgenerational constancy of epigenetic structure in three populations of the perennial herb Helleborus foetidus (Ranunculaceae). Single-locus and multilocus analyses revealed extensive epigenetic differentiation between sporophyte populations. Locus-by-locus comparisons of methylation status in individual sporophytes and descendant gametophytes showed that ~75% of epigenetic markers persisted unchanged through gametogenesis. In spite of some epigenetic reorganization taking place during gametogenesis, multilocus epigenetic differentiation between sporophyte populations was preserved in the subsequent gametophyte stage. In addition to illustrating the efficacy of applying the MSAP technique to paired plant-pollen DNA samples to investigate epigenetic gametic inheritance in wild plants, this paper suggests that epigenetic differentiation between adult plant populations of H. foetidus is likely to persist across generations.

  4. The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates.

    Directory of Open Access Journals (Sweden)

    Jonci N Wolff

    Full Text Available In most species mitochondrial DNA (mtDNA is inherited maternally in an apparently clonal fashion, although how this is achieved remains uncertain. Population genetic studies show not only that individuals can harbor more than one type of mtDNA (heteroplasmy but that heteroplasmy is common and widespread across a diversity of taxa. Females harboring a mixture of mtDNAs may transmit varying proportions of each mtDNA type (haplotype to their offspring. However, mtDNA variants are also observed to segregate rapidly between generations despite the high mtDNA copy number in the oocyte, which suggests a genetic bottleneck acts during mtDNA transmission. Understanding the size and timing of this bottleneck is important for interpreting population genetic relationships and for predicting the inheritance of mtDNA based disease, but despite its importance the underlying mechanisms remain unclear. Empirical studies, restricted to mice, have shown that the mtDNA bottleneck could act either at embryogenesis, oogenesis or both. To investigate whether the size and timing of the mitochondrial bottleneck is conserved between distant vertebrates, we measured the genetic variance in mtDNA heteroplasmy at three developmental stages (female, ova and fry in chinook salmon and applied a new mathematical model to estimate the number of segregating units (N(e of the mitochondrial bottleneck between each stage. Using these data we estimate values for mtDNA Ne of 88.3 for oogenesis, and 80.3 for embryogenesis. Our results confirm the presence of a mitochondrial bottleneck in fish, and show that segregation of mtDNA variation is effectively complete by the end of oogenesis. Considering the extensive differences in reproductive physiology between fish and mammals, our results suggest the mechanism underlying the mtDNA bottleneck is conserved in these distant vertebrates both in terms of it magnitude and timing. This finding may lead to improvements in our understanding of

  5. Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.

    Science.gov (United States)

    Wang, Gary P; Sherrill-Mix, Scott A; Chang, Kyong-Mi; Quince, Chris; Bushman, Frederic D

    2010-06-01

    Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5' untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5' UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.

  6. Patterns of post-glacial genetic differentiation in marginal populations of a marine microalga.

    Directory of Open Access Journals (Sweden)

    Pia Tahvanainen

    Full Text Available This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS sequences and Amplified Fragment Length Polymorphism (AFLP of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F(ST between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.

  7. Landscape genetics reveals inbreeding and genetic bottlenecks in the extremely rare short-globose cacti Mammillaria pectinifera (Cactaceae as a result of habitat fragmentation

    Directory of Open Access Journals (Sweden)

    Reyna Maya-García

    2017-02-01

    Full Text Available Mammillaria pectinifera is an endemic, short-globose cactus species, included in the IUCN list as a threatened species with only 18 remaining populations in the Tehuacán-Cuicatlán Valley in central Mexico. We evaluated the population genetic diversity and structure, connectivity, recent bottlenecks and population size, using nuclear microsatellites. M. pectinifera showed high genetic diversity but some evidence of heterozygote deficiency (FIS, recent bottlenecks in some populations and reductions in population size. Also, we found low population genetic differentiation and high values of connectivity for M. pectinifera, as the result of historical events of gene flow through pollen and seed dispersal. M. pectinifera occurs in sites with some degree of disturbance leading to the isolation of its populations and decreasing the levels of gene flow among them. Excessive deforestation also changes the original vegetation damaging the natural habitats. This species will become extinct if it is not properly preserved. Furthermore, this species has some ecological features that make them more vulnerable to disturbance such as a very low growth rates and long life cycles. We suggest in situ conservation to prevent the decrease of population sizes and loss of genetic diversity in the natural protected areas such as the Tehuacán-Cuicatlán Biosphere Reserve. In addition, a long-term ex situ conservation program is need to construct seed banks, and optimize seed germination and plant establishment protocols that restore disturbed habitats. Furthermore, creating a supply of living plants for trade is critical to avoid further extraction of plants from nature.

  8. Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula.

    Directory of Open Access Journals (Sweden)

    Eva Graciá

    Full Text Available The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus. In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species' demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species' pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals

  9. Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula

    Science.gov (United States)

    Graciá, Eva; Ortego, Joaquín; Godoy, José Antonio; Pérez-García, Juan Manuel; Blanco, Guillermo; del Mar Delgado, María; Penteriani, Vincenzo; Almodóvar, Irene; Botella, Francisco; Sánchez-Zapata, José Antonio

    2015-01-01

    The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70’s. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus). In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species’ demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species’ pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals on the

  10. Phonon bottleneck identification in disordered nanoporous materials

    Science.gov (United States)

    Romano, Giuseppe; Grossman, Jeffrey C.

    2017-09-01

    Nanoporous materials are a promising platform for thermoelectrics in that they offer high thermal conductivity tunability while preserving good electrical properties, a crucial requirement for high-efficiency thermal energy conversion. Understanding the impact of the pore arrangement on thermal transport is pivotal to engineering realistic materials, where pore disorder is unavoidable. Although there has been considerable progress in modeling thermal size effects in nanostructures, it has remained a challenge to screen such materials over a large phase space due to the slow simulation time required for accurate results. We use density functional theory in connection with the Boltzmann transport equation to perform calculations of thermal conductivity in disordered porous materials. By leveraging graph theory and regressive analysis, we identify the set of pores representing the phonon bottleneck and obtain a descriptor for thermal transport, based on the sum of the pore-pore distances between such pores. This approach provide a simple tool to estimate phonon suppression in realistic porous materials for thermoelectric applications and enhance our understanding of heat transport in disordered materials.

  11. Analysis of the genetic diversity and differentiation of Fenneropenaeus penicillatus populations using AFLP technology

    Science.gov (United States)

    Zhang, Guiling; Cao, Yuanyu; Li, Zhongbao; Chen, Jin; Zhao, Binli; Lei, Guanggao; Wang, Zhanlin

    2012-05-01

    Fenneropenaeus penicillatus (redtail shrimp) is an important marine commercial animal in China. Recently, its resources have been depleted rapidly as a result of, for example, over-exploitation and environmental degradation of spawning grounds. Therefore, we analyzed the genetic diversity and differentiation of nine wild populations of F. penicillatus of China (Ningde, Lianjiang, Putian, Xiamen, Quanzhou, Zhangpu, Dongshan, Nanao, and Shenzhen populations) by amplified fragment length polymorphism (AFLP) technology, to provide genetic information necessary for resource protection, rejuvenation, artificial breeding, and sustainable use of the resource. Eight AFLP primer pairs were used for amplification, and 508 bands were detected among the populations. The results show that the percentage of polymorphic loci ( P) ranged from 41.34% to 63.58%; the Nei's gene diversity ( H) of the populations was 0.119 4-0.230 5; and Shannon's Information Index ( I) was 0.184 1-0.342 5. These genetic data indicate that the genetic diversity of F. penicillatus was high. The genetic differentiation coefficient ( G ST=0.216 2) and gene flow ( N m=1.812 4) show that there was a high level of genetic differentiation and a moderate level of gene flow among populations. More studies on the genetic differentiation mechanism of F. penicillatus along the south-eastern coast of China need to be conducted to find more effective scientific protection strategies for the conservation of F. penicillatus genetic resources.

  12. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

    Science.gov (United States)

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T.; Morgan, Alex A.; Moreno-Estrada, Andres; Nilsen, Geoffrey B.; Ruau, David; Lincoln, Stephen E.; Bustamante, Carlos D.; Butte, Atul J.

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  13. Habitat Fragmentation Differentially Affects Genetic Variation, Phenotypic Plasticity and Survival in Populations of a Gypsum Endemic

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    2017-05-01

    Full Text Available Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia, a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population’s similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations’ survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness

  14. Microsatellite DNA reveals population genetic differentiation among sprat (Sprattus sprattus) sampled throughout the Northeast Atlantic, including Norwegian fjords

    DEFF Research Database (Denmark)

    Glover, Kevin A.; Skaala, Øystein; Limborg, Morten

    2011-01-01

    Glover, K. A., Skaala, Ø., Limborg, M., Kvamme, C., and Torstensen, E. Microsatellite DNA reveals population genetic differentiation among sprat (Sprattus sprattus) sampled throughout the Northeast Atlantic, including Norwegian fjords. – ICES Journal of Marine Science, 68: 2145–2151. Sprat (Sprat...... display population genetic differentiation throughout the Northeast Atlantic, and there may be limited connectivity between Norwegian fjord and sea-going populations....

  15. Molecular population genetics of the β-esterase gene cluster of ...

    Indian Academy of Sciences (India)

    We suggest that the demographic history (bottleneck and admixture of genetically differentiated populations) is the major factor shaping the pattern of nucleotide ... Biology, Vladivostok 690041, Russia, and Academy of Ecology, Marine Biology, and Biotechnology, Far Eastern State University, Vladivostok 690600, Russia ...

  16. A theory of traffic congestion at heavy bottlenecks

    Science.gov (United States)

    Kerner, Boris S.

    2008-05-01

    Spatiotemporal features and physics of vehicular traffic congestion occurring due to heavy highway bottlenecks caused for example by bad weather conditions or accidents are found based on simulations in the framework of three-phase traffic theory. A model of a heavy bottleneck is presented. Under a continuous non-limited increase in bottleneck strength, i.e., when the average flow rate within a congested pattern allowed by the heavy bottleneck decreases continuously up to zero, the evolution of the traffic phases in congested traffic, synchronized flow and wide moving jams, is studied. It is found that at a small enough flow rate within the congested pattern, the pattern exhibits a non-regular structure: a pinch region of synchronized flow within the pattern disappears and appears randomly over time; wide moving jams upstream of the pinch region exhibit a complex non-regular dynamics in which the jams appear and disappear randomly. At greater bottleneck strengths, wide moving jams merge onto a mega-wide moving jam (mega-jam) within which low-speed patterns with a complex non-regular spatiotemporal dynamics occur. We show that when the bottleneck strength is great enough, only the mega-jam survives and synchronized flow remains only within its downstream front separating free flow and congested traffic. Theoretical results presented can explain why no sequence of wide moving jams can often be distinguished in non-homogeneous traffic congestion measured at very heavy bottlenecks caused by bad weather conditions or accidents.

  17. Data prep: the bottleneck of future applications?

    Science.gov (United States)

    Gramss, Juergen; Eichhorn, Hans; Lempke, Melchior; Jaritz, Renate; Neick, Volker; Beyer, Dirk; Buerger, Bertram; Baetz, Ulrich; Kunze, Klaus; Belic, Nikola

    2006-06-01

    There is no doubt that shaped beam systems have been well established in the mask write community since the introduction of the 130nm technology node. Moreover, they are successfully advancing to conquer also the wafer direct write market. To be able to handle today and in the near future the tremendous data volumes with their characteristic complexity as well as to make use of such indispensable methods like PEC and Fogging corrections, new, sophisticated solutions are necessary to master the challenging 45nm technology node. However, we are aware that the 45nm node presents only an intermediate step, because, according to the international roadmap, we soon will be confronted with the hardware and software requirements of the next, the 32nm technology node. In this context it becomes more and more important to consider potential showstoppers, in our case the data preparation process To investigate this complex subject a Linux cluster computer featuring 3.6GHz clock rate CPUs, and a software package supporting distributed computing with a 64Bit version and address units down to 0.1nm were used. The work was focused on the performance of pattern samples down to the 45nm node. Both mask and wafer data as well as NIL template manufacturing were considered, data prep times and CPU loads were analysed. Furthermore, the user-friendly Leica Interface for Data Preparations (LINDA) was applied. In addition, an outlook to future hardware/software configurations for mastering the challenges of the 32nm node will be given. The results presented in this paper prove that data preparation is not the bottleneck of current and future applications.

  18. Deep bottleneck features for spoken language identification.

    Directory of Open Access Journals (Sweden)

    Bing Jiang

    Full Text Available A key problem in spoken language identification (LID is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF for spoken LID, motivated by the success of Deep Neural Networks (DNN in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV, using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09 show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed.

  19. [Comparison of differentiated thyroid carcinoma staging systems in a Spanish population].

    Science.gov (United States)

    Andía Melero, Víctor Manuel; Martín de Santa-Olalla Llanes, María; Sambo Salas, Marcel; Percovich Hualpa, Juan Carlos; Motilla de la Cámara, Marta; Collado Yurrita, Luis

    2015-04-01

    Differentiated thyroid carcinoma staging is increasingly important due to the current trends to a less intensive therapy in low-risk patients. The TNM system is most widely used, but other systems based on follow-up of several patient cohorts have been developed. When these systems have been applied to other populations, results have been discordant. Our study evaluates the suitability of several differentiated thyroid carcinoma staging systems in a Spanish population. 729 patients with differentiated thyroid carcinoma and staging data available were enrolled. Mean follow-up time was 10.8 years. The TNM, EORTC, AMES, Clinical class, MACIS, Ohio, NTCTCS, and Spanish systems were applied to all histological types. The Kaplan-Meier survival curves for each system were analyzed, and compared using the proportion of explained variation (PEV). The demographic and clinical characteristics of our population were similar to those of other Spanish and international cohorts reported. The best systems were NTCTCS, with 74.7% PEV, and TNM (68.3%), followed by the Ohio, MACIS, EORTC, and AMES systems with minimal differences between them, while the least adequate were the Spanish (55.2%) and Clinical class (47.1%) systems. The NTCTCS staging system was found to be better than TNM in our population but, because of its simplicity and greater dissemination, the TNM appears to be recommended for staging of patients with differentiated thyroid carcinoma. Copyright © 2014 SEEN. Published by Elsevier España, S.L.U. All rights reserved.

  20. Population of bottleneck and microsatellite: An Analysis Based on ...

    African Journals Online (AJOL)

    use

    2011-11-23

    Nov 23, 2011 ... 'Steps towards the implementation of a genetic improvement program for Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in Mexico. Acuicultura, 99(1): 279-286. Keller LF, Jeffery KJ, Arcese P, Beaumont MA, Hochachka WM, Smith. JNM, Bruford MW (2001). Immigration and the ephemerality of a.

  1. Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells.

    Science.gov (United States)

    Bargaje, Rhishikesh; Trachana, Kalliopi; Shelton, Martin N; McGinnis, Christopher S; Zhou, Joseph X; Chadick, Cora; Cook, Savannah; Cavanaugh, Christopher; Huang, Sui; Hood, Leroy

    2017-02-28

    Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or "tipping point" at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations.

  2. Genetic differentiation among natural populations of the Nile tilapia Oreochromis niloticus (Teleostei, cichlidae).

    Science.gov (United States)

    Agnèse, J F; Adépo-Gourène, B; Abban, E K; Fermon, Y

    1997-07-01

    We analysed the genetic differentiation among 17 natural populations of the Nile tilapia Oreochromis niloticus (Linnaeus, 1758) using allozymes and restriction fragment length polymorphism (RFLP) of mitochondrial DNA (mtDNA). The populations studied, from the River Senegal to Lake Tana and from Lake Manzalla to Lake Baringo, represent all subspecies which have been previously described. Sixteen variable nuclear loci showed that these populations can be clustered in three groups: (1) West African populations (Senegal, Niger, Volta and Chad drainages), (2) Ethiopian Rift Valley populations (Lakes Awasa, Ziway, Koka and the Awash River) and (3) Nile drainage (Manzalla, Cairo, Lake Edward) and Kenyan Rift Valley populations (Lakes Turkana, Baringo and River Suguta). Nine different mtDNA haplotypes were found in the RFLP analysis of a 1 kb portion of the D-loop region. The network obtained showed that there are three geographically distinct groups; all West African populations and O. aureus are clustered, the two Ethiopian Rift Valley populations are distinct and between these two groups are the Kenyan and Ugandan Rift Valley populations. Nile populations show affinities both with West African populations and with specimens from Lakes Tana and Turkana. Taxonomic and biogeographical implications of these results are discussed.

  3. Microgeographic differentiation in thermal performance curves between rural and urban populations of an aquatic insect.

    Science.gov (United States)

    Tüzün, Nedim; Op de Beeck, Lin; Brans, Kristien I; Janssens, Lizanne; Stoks, Robby

    2017-12-01

    The rapidly increasing rate of urbanization has a major impact on the ecology and evolution of species. While increased temperatures are a key aspect of urbanization ("urban heat islands"), we have very limited knowledge whether this generates differentiation in thermal responses between rural and urban populations. In a common garden experiment, we compared the thermal performance curves (TPCs) for growth rate and mortality in larvae of the damselfly Coenagrion puella from three urban and three rural populations. TPCs for growth rate shifted vertically, consistent with the faster-slower theoretical model whereby the cold-adapted rural larvae grew faster than the warm-adapted urban larvae across temperatures. In line with costs of rapid growth, rural larvae showed lower survival than urban larvae across temperatures. The relatively lower temperatures hence expected shorter growing seasons in rural populations compared to the populations in the urban heat islands likely impose stronger time constraints to reach a certain developmental stage before winter, thereby selecting for faster growth rates. In addition, higher predation rates at higher temperature may have contributed to the growth rate differences between urban and rural ponds. A faster-slower differentiation in TPCs may be a widespread pattern along the urbanization gradient. The observed microgeographic differentiation in TPCs supports the view that urbanization may drive life-history evolution. Moreover, because of the urban heat island effect, urban environments have the potential to aid in developing predictions on the impact of climate change on rural populations.

  4. Derivation of stochastic partial differential equations for size- and age-structured populations.

    Science.gov (United States)

    Allen, Edward J

    2009-01-01

    Stochastic partial differential equations (SPDEs) for size-structured and age- and size-structured populations are derived from basic principles, i.e. from the changes that occur in a small time interval. Discrete stochastic models of size-structured and age-structured populations are constructed, carefully taking into account the inherent randomness in births, deaths, and size changes. As the time interval decreases, the discrete stochastic models lead to systems of Itô stochastic differential equations. As the size and age intervals decrease, SPDEs are derived for size-structured and age- and size-structured populations. Comparisons between numerical solutions of the SPDEs and independently formulated Monte Carlo calculations support the accuracy of the derivations.

  5. Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor.

    Science.gov (United States)

    Hamblin, Martha T; Casa, Alexandra M; Sun, Hong; Murray, Seth C; Paterson, Andrew H; Aquadro, Charles F; Kresovich, Stephen

    2006-06-01

    Multilocus surveys of sequence variation can be used to identify targets of directional selection, which are expected to have reduced levels of variation. Following a population bottleneck, the signal of directional selection may be hard to detect because many loci may have low variation by chance and the frequency spectrum of variation may be perturbed in ways that resemble the effects of selection. Cultivated Sorghum bicolor contains a subset of the genetic diversity found in its wild ancestor(s) due to the combined effects of a domestication bottleneck and human selection on traits associated with agriculture. As a framework for distinguishing between the effects of demography and selection, we sequenced 204 loci in a diverse panel of 17 cultivated S. bicolor accessions. Genomewide patterns of diversity depart strongly from equilibrium expectations with regard to the variance of the number of segregating sites, the site frequency spectrum, and haplotype configuration. Furthermore, gene genealogies of most loci with an excess of low frequency variants and/or an excess of segregating sites do not show the characteristic signatures of directional and diversifying selection, respectively. A simple bottleneck model provides an improved but inadequate fit to the data, suggesting the action of other population-level factors, such as population structure and migration. Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model.

  6. Overcoming gaps and bottlenecks to advance precision agriculture

    Science.gov (United States)

    Maintaining a clear understanding of the technology gaps, knowledge needs, and training bottlenecks is required for improving adoption of precision agriculture. As an industry, precision agriculture embraces tools, methods, and practices that are constantly changing, requiring industry, education, a...

  7. Ecological differentiation of Lemna minor L. and Spirodela polyrrhiza (L. Schleiden populations

    Directory of Open Access Journals (Sweden)

    Hanna Wożakowska-Natkaniec

    2015-01-01

    Full Text Available The subject of thep resent study are 19 natural, ecological populations of Lemna minor and Spirodela polyrrhiza coming from sixteen habitats in Lower Silesia. The study showed the essential differences between ecological populations of both species, conditioned on chemistry (pH, level N, P, K, Ca, Mg and Fe and the natural water radioactivity. It was shown experimentally that these populations, in nature, establish a set of ecotypes or ecophene variability. Ecotypic differentiation of populations of Lemna minor and Spirodela polyrrhiza is based upon individual features and population characteristics such as: shape and size of plants, plant frequency of two, three, and four fronds, the ratio of right- to left-handed plants, and the dynamics of growth and biomass production.

  8. Research of Cruise Industry Development Bottlenecks In China

    OpenAIRE

    Ping Zhou

    2014-01-01

    Cruise industry is a comprehensive new industry, which has a strong impetus to the development of other industries. In recent years, as the explosive growth in cruise market, China has become a global rapidly-growing emerging cruise market. The cruise industry has begun transiting from infancy to the development phase, in all likelihood facing a number of bottlenecks problem. In this paper, the development trend of the cruise industry is first analyzed, then the bottlenecks of cruise industry...

  9. Analysis of moving bottlenecks considering a triangular fundamental diagram

    Directory of Open Access Journals (Sweden)

    Karim Fadhloun

    2016-10-01

    Full Text Available A significant number of research efforts have studied and analyzed the case in which a vehicle is moving slower than the traffic stream. This phenomenon, known as a moving bottleneck, results in a disruption of traffic flow and may significantly impact the traffic stream behavior upstream, downstream and abreast the slow moving vehicle. In this paper, a macroscopic approach for modeling moving bottlenecks is developed using microscopically derived data considering a triangular fundamental diagram. The passing flow rates of different moving bottleneck scenarios are determined using a previously developed microscopic model based on simulated data derived from the INTEGRATION software. Using the simulation results, an explicit expression of the bottleneck diagram, a flow-density relationship that defines the phenomenon macroscopically is proposed and the behavior of the traffic stream downstream and abreast the moving obstruction is depicted. It is demonstrated that the behavior of the traffic stream downstream of the slow vehicle as well as the acceleration behavior while passing is governed by the demand level. Such a result is coherent and consistent, to a significant extent, with two decades of research related to modeling moving bottlenecks and constitutes a potential feasible and more detailed description of the phenomenon in the case of a triangular fundamental diagram. Finally, it is noteworthy that the research subject of this paper could be considered as a first step in developing a numerical and practitioner-friendly framework for the analysis of moving bottlenecks that does not involve approaching the problem from its theoretical perspective.

  10. Local environment but not genetic differentiation influences biparental care in ten plover populations.

    Directory of Open Access Journals (Sweden)

    Orsolya Vincze

    Full Text Available Social behaviours are highly variable between species, populations and individuals. However, it is contentious whether behavioural variations are primarily moulded by the environment, caused by genetic differences, or a combination of both. Here we establish that biparental care, a complex social behaviour that involves rearing of young by both parents, differs between closely related populations, and then test two potential sources of variation in parental behaviour between populations: ambient environment and genetic differentiation. We use 2904 hours behavioural data from 10 geographically distinct Kentish (Charadrius alexandrinus and snowy plover (C. nivosus populations in America, Europe, the Middle East and North Africa to test these two sources of behavioural variation. We show that local ambient temperature has a significant influence on parental care: with extreme heat (above 40 °C total incubation (i.e. % of time the male or female incubated the nest increased, and female share (% female share of incubation decreased. By contrast, neither genetic differences between populations, nor geographic distances predicted total incubation or female's share of incubation. These results suggest that the local environment has a stronger influence on a social behaviour than genetic differentiation, at least between populations of closely related species.

  11. Nucleotide diversity and population differentiation of the Melanocortin 1 Receptor gene, MC1R

    Directory of Open Access Journals (Sweden)

    Peris Ketty

    2008-04-01

    Full Text Available Abstract Background The melanocortin 1 receptor gene (MC1R is responsible for normal pigment variation in humans and is highly polymorphic with numerous population-specific alleles. Some MC1R variants have been associated with skin cancer risk. Results Allele frequency data were compiled on 55 single nucleotide polymorphisms from seven geographically distinct human populations (n = 2306 individuals. MC1R nucleotide diversity, π, was much higher (10.1 × 10-4 than in other genes for all subjects. A large degree of population differentiation, determined by FST, was also present, particularly between Asia and all other populations, due to the p.R163Q (c.488 G>A polymorphism. The least amount of differentiation was between the United States, Northern Europe, and Southern Europe. Tajima's D statistic suggested the presence of positive selection in individuals from Europe. Conclusion This study further quantifies the degree of population-specific genetic variation and suggests that positive selection may be present in European populations in MC1R.

  12. Periodic solutions of first-order functional differential equations in population dynamics

    CERN Document Server

    Padhi, Seshadev; Srinivasu, P D N

    2014-01-01

    This book provides cutting-edge results on the existence of multiple positive periodic solutions of first-order functional differential equations. It demonstrates how the Leggett-Williams fixed-point theorem can be applied to study the existence of two or three positive periodic solutions of functional differential equations with real-world applications, particularly with regard to the Lasota-Wazewska model, the Hematopoiesis model, the Nicholsons Blowflies model, and some models with Allee effects. Many interesting sufficient conditions are given for the dynamics that include nonlinear characteristics exhibited by population models. The last chapter provides results related to the global appeal of solutions to the models considered in the earlier chapters. The techniques used in this book can be easily understood by anyone with a basic knowledge of analysis. This book offers a valuable reference guide for students and researchers in the field of differential equations with applications to biology, ecology, a...

  13. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L.

    Directory of Open Access Journals (Sweden)

    Juan C Motamayor

    Full Text Available Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.

  14. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L).

    Science.gov (United States)

    Motamayor, Juan C; Lachenaud, Philippe; da Silva E Mota, Jay Wallace; Loor, Rey; Kuhn, David N; Brown, J Steven; Schnell, Raymond J

    2008-10-01

    Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.

  15. Morphological and molecular differentiation of the croatian populations of Ouercus pubescens Willd. (Fagaceae

    Directory of Open Access Journals (Sweden)

    Josip Franjić

    2011-01-01

    Full Text Available Taxonomy of the genus Quercus L. is very complicated and often controversial because of its great variability and intense gene flow among the related species. The purpose of this research was to determine morphological and molecular variation, relationships and taxonomic status of the Croatian populations of Quercus pubescens Willd. using morphological analysis of the leaves and RAPD-PCR technique. The results of the morphological and molecular analyses were very similar, both showing differentiation of the southern (Mediterranean from the northern (Continental pubescent oak populations. These two groups were clearly separated and the estimated gene flow among the populations that belong to different groups (Nm=1.38 is significantly less than among the populations that belong to the same group (Nm=3.70. The obtained results were compared to the available studies. This study confirms a high variability of the Q. pubescens populations, but differences were not so big to confirm the opinion of existence of several species in this area. The conclusion is that the southern Croatian populations could be pure Q. pubescens populations, while the peculiarities of the northern Croatian populations originate probably from the Q. petraea introgression.

  16. Optimal Vaccine Distribution Strategy for Different Age Groups of Population: A Differential Evolution Algorithm Approach

    OpenAIRE

    Xiao-Min Hu; Jun Zhang; Haihong Chen

    2014-01-01

    Vaccination is one of the effective ways for protecting susceptible individuals from infectious diseases. Different age groups of population have different vulnerability to the disease and different contact frequencies. In order to achieve the maximum effects, the distribution of vaccine doses to the groups of individuals needs to be optimized. In this paper, a differential evolution (DE) algorithm is proposed to address the problem. The performance of the proposed algorithm has been tested b...

  17. Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehirae Hay. (Lauraceae in Taiwan inferred from nuclear genes

    Directory of Open Access Journals (Sweden)

    Ho Kuo-Chieh

    2010-04-01

    Full Text Available Abstract Background Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM is critically important for the conservation of this species. Results Populations of C. kanehirae were classified into four geographic regions: northwestern (NW, west-central (WC, southwestern (SW, and southeastern (SE. In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs intron and leafy (Lfy intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples. Conclusions Common haplotype distributions among geographic regions and the relatively

  18. Derivation of keratinocytes from chicken embryonic stem cells: Establishment and characterization of differentiated proliferative cell populations

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    Mathilde Couteaudier

    2015-03-01

    Full Text Available A common challenge in avian cell biology is the generation of differentiated cell-lines, especially in the keratinocyte lineage. Only a few avian cell-lines are available and very few of them show an interesting differentiation profile. During the last decade, mammalian embryonic stem cell-lines were shown to differentiate into almost all lineages, including keratinocytes. Although chicken embryonic stem cells had been obtained in the 1990s, few differentiation studies toward the ectodermal lineage were reported. Consequently, we explored the differentiation of chicken embryonic stem cells toward the keratinocyte lineage by using a combination of stromal induction, ascorbic acid, BMP4 and chicken serum. During the induction period, we observed a downregulation of pluripotency markers and an upregulation of epidermal markers. Three homogenous cell populations were derived, which were morphologically similar to chicken primary keratinocytes, displaying intracellular lipid droplets in almost every pavimentous cell. These cells could be serially passaged without alteration of their morphology and showed gene and protein expression profiles of epidermal markers similar to chicken primary keratinocytes. These cells represent an alternative to the isolation of chicken primary keratinocytes, being less cumbersome to handle and reducing the number of experimental animals used for the preparation of primary cells.

  19. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

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    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  20. Genetic Diversity and Population Differentiation of Guignardia mangiferae from “Tahiti” Acid Lime

    Science.gov (United States)

    Wickert, Ester; Lemos, Eliana Gertrudes de Macedo; Kishi, Luciano Takeshi; de Souza, Andressa; de Goes, Antonio

    2012-01-01

    Among the citrus plants, “Tahiti” acid lime is known as a host of G. mangiferae fungi. This species is considered endophytic for citrus plants and is easily isolated from asymptomatic fruits and leaves. G. mangiferae is genetically related and sometimes confused with G. citricarpa which causes Citrus Black Spot (CBS). “Tahiti” acid lime is one of the few species that means to be resistant to this disease because it does not present symptoms. Despite the fact that it is commonly found in citric plants, little is known about the populations of G. mangiferae associated with these plants. Hence, the objective of this work was to gain insights about the genetic diversity of the G. mangiferae populations that colonize “Tahiti” acid limes by sequencing cistron ITS1-5.8S-ITS2. It was verified that “Tahiti” acid lime plants are hosts of G. mangiferae and also of G. citricarpa, without presenting symptoms of CBS. Populations of G. mangiferae present low-to-moderate genetic diversity and show little-to-moderate levels of population differentiation. As gene flow was detected among the studied populations and they share haplotypes, it is possible that all populations, from citrus plants and also from the other known hosts of this fungus, belong to one great panmictic population. PMID:22619579

  1. Genetic diversity and population differentiation of Guignardia mangiferae from "Tahiti" acid lime.

    Science.gov (United States)

    Wickert, Ester; de Macedo Lemos, Eliana Gertrudes; Kishi, Luciano Takeshi; de Souza, Andressa; de Goes, Antonio

    2012-01-01

    Among the citrus plants, "Tahiti" acid lime is known as a host of G. mangiferae fungi. This species is considered endophytic for citrus plants and is easily isolated from asymptomatic fruits and leaves. G. mangiferae is genetically related and sometimes confused with G. citricarpa which causes Citrus Black Spot (CBS). "Tahiti" acid lime is one of the few species that means to be resistant to this disease because it does not present symptoms. Despite the fact that it is commonly found in citric plants, little is known about the populations of G. mangiferae associated with these plants. Hence, the objective of this work was to gain insights about the genetic diversity of the G. mangiferae populations that colonize "Tahiti" acid limes by sequencing cistron ITS1-5.8S-ITS2. It was verified that "Tahiti" acid lime plants are hosts of G. mangiferae and also of G. citricarpa, without presenting symptoms of CBS. Populations of G. mangiferae present low-to-moderate genetic diversity and show little-to-moderate levels of population differentiation. As gene flow was detected among the studied populations and they share haplotypes, it is possible that all populations, from citrus plants and also from the other known hosts of this fungus, belong to one great panmictic population.

  2. Genetic Diversity and Population Differentiation of Guignardia mangiferae from “Tahiti” Acid Lime

    Directory of Open Access Journals (Sweden)

    Ester Wickert

    2012-01-01

    Full Text Available Among the citrus plants, “Tahiti” acid lime is known as a host of G. mangiferae fungi. This species is considered endophytic for citrus plants and is easily isolated from asymptomatic fruits and leaves. G. mangiferae is genetically related and sometimes confused with G. citricarpa which causes Citrus Black Spot (CBS. “Tahiti” acid lime is one of the few species that means to be resistant to this disease because it does not present symptoms. Despite the fact that it is commonly found in citric plants, little is known about the populations of G. mangiferae associated with these plants. Hence, the objective of this work was to gain insights about the genetic diversity of the G. mangiferae populations that colonize “Tahiti” acid limes by sequencing cistron ITS1-5.8S-ITS2. It was verified that “Tahiti” acid lime plants are hosts of G. mangiferae and also of G. citricarpa, without presenting symptoms of CBS. Populations of G. mangiferae present low-to-moderate genetic diversity and show little-to-moderate levels of population differentiation. As gene flow was detected among the studied populations and they share haplotypes, it is possible that all populations, from citrus plants and also from the other known hosts of this fungus, belong to one great panmictic population.

  3. Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis.

    Science.gov (United States)

    Cardoso, S R; Eloy, N B; Provan, J; Cardoso, M A; Ferreira, P C

    2000-11-01

    Heart-of-palm (Euterpe edulis Mart.) is a wild palm with a wide distribution throughout the Atlantic Rainforest. Populations of E. edulis represent important renewable natural resources but are currently under threat from predatory exploitation. Furthermore, because the species is indigenous to the Atlantic Rainforest, which is located in the most economically developed and populated region of Brazil, social and economic pressures have devastated heart-of-palm forests. In order to estimate the partitioning of genetic variation of endangered E. edulis populations, 429 AFLP markers were used to analyse 150 plants representing 11 populations of the species distribution range. Analysis of the genetic structure of populations carried out using analysis of molecular variance (AMOVA) revealed moderate genetic variation within populations (57. 4%). Genetic differentiation between populations (FST = 0.426) was positively correlated with geographical distance. These results could be explained by the historical fragmentation of the Atlantic coastal region, together with the life cycle and mating system. The data obtained in this work should have important implications for conservation and future breeding programmes of E. edulis.

  4. Bottlenecks in serial production lines: A system-theoretic approach

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    C.-T. Kuo

    1996-01-01

    Full Text Available In this work, a new definition of production systems bottlenecks is formulated and analyzed. Specifically, a machine is defined as the bottleneck if the sensitivity of the system's performance index to this machine's production rate in isolation is the largest. Although appealing from the systems point of view, this definition suffers a deficiency due to the fact that the sensitivities involved cannot be either measured on-line or efficiently calculated off-line. To avoid this, the paper develops a method based on indirect but real-time data. From this point of view, the main result of the work is as follows: The bottleneck machine in a serial production line can be identified by analyzing relationships between the so-called manufacturing blockage and manufacturing starvation of each machine. This leads to a simple rule for bottleneck identification. The rule requires neither the calculation of the production rate sensitivities nor the production rate itself. When the probabilities of manufacturing blockages and starvations are not available from on-line measurements, the paper presents their analytical estimates which, under certain conditions, can be used for bottleneck identification. Finally, a case study at an automotive component plant is described.

  5. Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

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    Małgorzata Pilot

    Full Text Available Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13C and δ(15N values for Eastern European wolves (Canis lupus as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure, to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.

  6. Evidence of morphometric differentiation among Antarctic moss populations as a response to local microenvironment

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    Rayssa Garay Medina

    2015-09-01

    Full Text Available ABSTRACTStudies on phenotypic variation among populations growing in different microenvironments may provide information about plasticity related to environmental pressures, and thus help to elucidate the potential evolutionary forces contributing to the origin and maintenance of diversity in any region. In this study we investigate morphometric variation on a small geographic scale for three species of Antarctic mosses. All species revealed significant differentiation among populations for all evaluated traits. The comparison of morphometric measures of populations of Polytrichum juniperinumfrom Nelson Island and from southern Brazil suggests that the effects of a small geographic scale in Antarctica are the same as a large geographic scale in environments where the climate is more homogeneous and microhabitats have minor influence on vegetation. However, further investigations over a larger area, evaluating more species, and using controlled garden experiments are recommended in order to evaluate the capacity for plasticity of moss species in different climatic conditions and on different geographic scales.

  7. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

    Science.gov (United States)

    Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

    2016-01-01

    Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among

  8. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

    Directory of Open Access Journals (Sweden)

    Shabnam Abbasi

    Full Text Available Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros and desert zones (Kavir, with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU. At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was

  9. Spatially differentiated and source-specific population exposure to ambient urban air pollution

    Science.gov (United States)

    Zou, Bin; Wilson, J. Gaines; Zhan, F. Benjamin; Zeng, Yongnian

    Models assessing exposure to air pollution often focus on macro-scale estimates of exposure to all types of sources for a particular pollutant across an urban study area. While results based on these models may aid policy makers in identifying larger areas of elevated exposure risk, they often do not differentiate the proportion of population exposure attributable to different polluting sources (e.g. traffic or industrial). In this paper, we introduce a population exposure modeling system that integrates air dispersion modeling, Geographic Information Systems (GIS), and population exposure techniques to spatially characterize a source-specific exposure to ambient air pollution for an entire urban population at a fine geographical scale. By area, total population exposure in Dallas County in 2000 was more attributable to vehicle polluting sources than industrial polluting sources at all levels of exposure. Population exposure was moderately correlated with vehicle sources ( r = 0.440, p modeling system proposed in this study shows promise for use by municipal authorities, policy makers, and epidemiologists in evaluating and controlling the quality of the air in the process of urban planning and mitigation measures.

  10. Genetic diversity and population differentiation of the causal agent of citrus black spot in Brazil.

    Science.gov (United States)

    Wickert, Ester; de Goes, Antonio; de Souza, Andressa; Lemos, Eliana Gertrudes de Macedo

    2012-01-01

    One of the most important diseases that affect sweet orange orchards in Brazil is the Citrus Black Spot that is caused by the fungus Guignardia citricarpa. This disease causes irreparable losses due to the premature falling of fruit, as well as its severe effects on the epidermis of ripe fruit that renders them unacceptable at the fresh fruit markets. Despite the fact that the fungus and the disease are well studied, little is known about the genetic diversity and the structure of the fungi populations in Brazilian orchards. The objective of this work was study the genetic diversity and population differentiation of G. citricarpa associated with four sweet orange varieties in two geographic locations using DNA sequence of ITS1-5.8S-ITS2 region from fungi isolates. We observed that different populations are closely related and present little genetic structure according to varieties and geographic places with the highest genetic diversity distributed among isolates of the same populations. The same haplotypes were sampled in different populations from the same and different orange varieties and from similar and different origins. If new and pathogenic fungi would become resistant to fungicides, the observed genetic structure could rapidly spread this new form from one population to others.

  11. Genetic Diversity and Population Differentiation of the Causal Agent of Citrus Black Spot in Brazil

    Directory of Open Access Journals (Sweden)

    Ester Wickert

    2012-01-01

    Full Text Available One of the most important diseases that affect sweet orange orchards in Brazil is the Citrus Black Spot that is caused by the fungus Guignardia citricarpa. This disease causes irreparable losses due to the premature falling of fruit, as well as its severe effects on the epidermis of ripe fruit that renders them unacceptable at the fresh fruit markets. Despite the fact that the fungus and the disease are well studied, little is known about the genetic diversity and the structure of the fungi populations in Brazilian orchards. The objective of this work was study the genetic diversity and population differentiation of G. citricarpa associated with four sweet orange varieties in two geographic locations using DNA sequence of ITS1-5.8S-ITS2 region from fungi isolates. We observed that different populations are closely related and present little genetic structure according to varieties and geographic places with the highest genetic diversity distributed among isolates of the same populations. The same haplotypes were sampled in different populations from the same and different orange varieties and from similar and different origins. If new and pathogenic fungi would become resistant to fungicides, the observed genetic structure could rapidly spread this new form from one population to others.

  12. Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation.

    Science.gov (United States)

    Carreras, Carlos; Ordóñez, Víctor; Zane, Lorenzo; Kruschel, Claudia; Nasto, Ina; Macpherson, Enrique; Pascual, Marta

    2017-03-06

    The assessment of the genetic structuring of biodiversity is crucial for management and conservation. For species with large effective population sizes a low number of markers may fail to identify population structure. A solution of this shortcoming can be high-throughput sequencing that allows genotyping thousands of markers on a genome-wide approach while facilitating the detection of genetic structuring shaped by selection. We used Genotyping-by-Sequencing (GBS) on 176 individuals of the endemic East Atlantic peacock wrasse (Symphodus tinca), from 6 locations in the Adriatic and Ionian seas. We obtained a total of 4,155 polymorphic SNPs and we observed two strong barriers to gene flow. The first one differentiated Tremiti Islands, in the northwest, from all the other locations while the second one separated east and south-west localities. Outlier SNPs potentially under positive selection and neutral SNPs both showed similar patterns of structuring, although finer scale differentiation was unveiled with outlier loci. Our results reflect the complexity of population genetic structure and demonstrate that both habitat fragmentation and positive selection are on play. This complexity should be considered in biodiversity assessments of different taxa, including non-model yet ecologically relevant organisms.

  13. Herbivory at marginal populations: Consequences for maternal fitness and vegetative differentiation

    Science.gov (United States)

    Castilla, Antonio R.; Alonso, Conchita; Herrera, Carlos M.

    2013-05-01

    Margins of distribution of plant species constitute natural areas where the impact of the antagonistic interactions is expected to be higher and where changes in the dynamics of plant-herbivore coevolution could promote intraspecific differentiation in (co)evolving plant traits. In the present study, we investigated how differences in the average herbivory level affect maternal fitness in core continuous and marginal disjunct populations of Daphne laureola in an effort to assess the role of herbivores limiting plant distribution. Furthermore, we investigated intraspecific differentiation in vegetative traits and their potential connection to divergent selection by herbivores in both groups of populations. Our results did not support increased herbivory at the species margin but did support a difference in the effect of herbivory on maternal fitness between core continuous and marginal disjunct populations of D. laureola. In addition, herbivores did not exert phenotypic selection consistent with the geographic variation in studied plant traits. Therefore, the geographic variation of vegetative traits of D. laureola seems to be consequence of environmental heterogeneity more than result of geographically divergent selection by herbivores.

  14. Plant population differentiation and climate change: responses of grassland species along an elevational gradient.

    Science.gov (United States)

    Frei, Esther R; Ghazoul, Jaboury; Matter, Philippe; Heggli, Martin; Pluess, Andrea R

    2014-02-01

    Mountain ecosystems are particularly susceptible to climate change. Characterizing intraspecific variation of alpine plants along elevational gradients is crucial for estimating their vulnerability to predicted changes. Environmental conditions vary with elevation, which might influence plastic responses and affect selection pressures that lead to local adaptation. Thus, local adaptation and phenotypic plasticity among low and high elevation plant populations in response to climate, soil and other factors associated with elevational gradients might underlie different responses of these populations to climate warming. Using a transplant experiment along an elevational gradient, we investigated reproductive phenology, growth and reproduction of the nutrient-poor grassland species Ranunculus bulbosus, Trifolium montanum and Briza media. Seeds were collected from low and high elevation source populations across the Swiss Alps and grown in nine common gardens at three different elevations with two different soil depths. Despite genetic differentiation in some traits, the results revealed no indication of local adaptation to the elevation of population origin. Reproductive phenology was advanced at lower elevation in low and high elevation populations of all three species. Growth and reproduction of T. montanum and B. media were hardly affected by garden elevation and soil depth. In R. bulbosus, however, growth decreased and reproductive investment increased at higher elevation. Furthermore, soil depth influenced growth and reproduction of low elevation R. bulbosus populations. We found no evidence for local adaptation to elevation of origin and hardly any differences in the responses of low and high elevation populations. However, the consistent advanced reproductive phenology observed in all three species shows that they have the potential to plastically respond to environmental variation. We conclude that populations might not be forced to migrate to higher elevations

  15. Differential impact of tobacco control policies on youth sub-populations.

    Science.gov (United States)

    Tauras, John A; Huang, Jidong; Chaloupka, Frank J

    2013-09-12

    While previous studies have demonstrated the efficacy of tobacco control interventions in reducing tobacco use among youth overall, there have been very few studies that examine the potential differential impact of tobacco control policies on various youth subgroups, defined by socio-economic status (SES), race/ethnicity, and gender. We examined the relationship between state-level cigarette prices and smoke-free air laws and youth smoking prevalence and intensity for various youth sub-populations in the United States. We estimated a 2-part model of cigarette demand using data from the 1991 through 2010 nationally representative surveys of 8th-, 10th-, and 12th-grade students as part of the Monitoring the Future project. We found that real cigarette prices are strong determinants of youth smoking. Blacks, females, Hispanics, and low-SES subpopulations are found to have a larger price response with respect to smoking prevalence than the full sample. Smoke-free air laws are found to have a negative effect on smoking prevalence for the full sample and for the male, white, and high-SES sub-populations. This research concludes that higher cigarette prices will reduce smoking prevalence rates of Blacks, Hispanics, females, and low-SES subpopulations faster than the overall youth population and other youth sub-populations. Moreover, this research concludes that smoke-free air laws will reduce smoking prevalence for the overall youth population with the largest reductions in high SES and male subpopulations.

  16. Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda.

    Science.gov (United States)

    Musoli, P; Cubry, P; Aluka, P; Billot, C; Dufour, M; De Bellis, F; Pot, D; Bieysse, D; Charrier, A; Leroy, T

    2009-07-01

    Coffea canephora Pierre ex Frohener is a perennial plant originated from Africa. Two main groups, Guinean and Congolese, have already been identified within this species. They correspond to main refugia in western and central Africa. In this paper we present the analysis of a region that has not yet been studied, Uganda. Two wild, one feral (once cultivated but abandoned for many years), and two cultivated populations of C. canephora from Uganda were evaluated using 24 microsatellite markers. Basic diversity, dissimilarity and genetic distances between individuals, genetic differentiation between populations, and structure within populations were analysed. Expected heterozygosity was high for wild compartments (0.48 to 0.54) and for cultivated and feral ones (0.57 to 0.59), with the number of private alleles ranging from 12 for cultivated genotypes to 37 for a wild compartment. The Ugandan samples show significant population structuring. We compared the Ugandan populations with a representative sample of known genetic diversity groups within the species using 18 markers. Coffea canephora of Ugandan origin was found to be genetically different from previously identified diversity groups, implying that it forms another diversity group within the species. Given its large distribution and extremely recent domestication, C. canephora can be used to understand the effect of refugia colonization on genetic diversity.

  17. TPO genetic variants and risk of differentiated thyroid carcinoma in two European populations.

    Science.gov (United States)

    Cipollini, Monica; Pastor, Susana; Gemignani, Federica; Castell, Juan; Garritano, Sonia; Bonotti, Alessandra; Biarnés, Josefina; Figlioli, Gisella; Romei, Cristina; Marcos, Ricard; Cristaudo, Alfonso; Elisei, Rossella; Landi, Stefano; Velázquez, Antonia

    2013-12-15

    Thyroid cancer risk involves the interaction of genetic and environmental factors. The thyroperoxidase (TPO) has a key role in the iodine metabolism, being essential for the thyroid function. Mutations in the TPO gene are common in congenital hypothyroidism, and there are also signs of the implication of TPO in thyroid cancer. We performed a case-control association study of genetic variants in TPO and differentiated thyroid carcinoma (DTC) in 1,586 DTC patients and 1,769 controls including two European populations (Italy: 1,190 DTC and 1,290 controls; Spain: 396 DTC and 479 controls). Multivariate logistic regression analyses were performed separately for each population and each single-nucleotide polymorphism (SNP). From the three studied polymorphisms, significant associations were detected between DTC and rs2048722 and rs732609 in both populations (p TPO polymorphism in the Italian and the Spanish populations. Our results, for the first time, point to TPO as a gene involved in the risk of DTC, and suggest the importance of interactions between TPO variants and other unidentified population-specific factors in determining thyroid cancer risk. Copyright © 2013 UICC.

  18. Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes.

    Science.gov (United States)

    Congdon, B C; Piatt, J F; Martin, K; Friesen, V L

    2000-06-01

    Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum-likelihood analysis of allele frequencies suggested that murrelets from "mainland" sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation-by-distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early-mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands.

  19. Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes

    Science.gov (United States)

    Congdon, B.C.; Piatt, John F.; Martin, Kathy; Friesen, Vicki L.

    2000-01-01

    Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum-likelihood analysis of allele frequencies suggested that murrelets from 'mainland' sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation-by-distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early-mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands.

  20. Ancient geographical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. lanceolata

    Directory of Open Access Journals (Sweden)

    Yuchen Yang

    2016-10-01

    Full Text Available Glacial vicariance is thought to influence population dynamics and speciation of many marine organisms. Mangroves, a plant group inhabiting intertidal zones, were also profoundly influenced by Pleistocene glaciations. In this study, we investigated phylogeographic patterns of a widespread mangrove species Sonneratia caseolaris and a narrowly distributed, closely related species S. lanceolata to infer their divergence histories and related it to historical geological events. We sequenced two chloroplast fragments and five nuclear genes for one population of S. lanceolata and 12 populations of S. caseolaris across the Indo-West Pacific (IWP region to evaluate genetic differentiation and divergence time among them. Phylogenetic analysis based on sequences of nuclear ribosomal internal transcribed spacer (nrITS and a nuclear gene rpl9 for all Sonneratia species indicate that S. lanceolata individuals are nested within S. caseolaris. We found strong genetic structure among geographic regions (South China Sea, the Indian Ocean and eastern Australia inhabited by S. caseolaris. We estimated that divergence between the Indo-Malesia and Australasia populations occurred 4.035 million years ago (MYA, prior to the onset of Pleistocene. BARRIERS analysis suggested that complex geographic features in the IWP region had largely shaped the phylogeographic patterns of S. caseolaris. Furthermore, haplotype analyses provided convincing evidence for secondary contact of the South China Sea (SCS and the Indian Ocean lineages at the Indo-Pacific boundary. Demographic history inference under isolation and migration (IM model detected substantial gene flow from the Sri Lanka populations to the populations in the Java Island. Moreover, multi-locus sequence analysis indicated that S. lanceolata was most closely related to the Indian Ocean populations of S. caseolaris and the divergence time between them was 2.057 MYA, coinciding with the onset of the Pleistocene

  1. Individualism in plant populations: using stochastic differential equations to model individual neighbourhood-dependent plant growth.

    Science.gov (United States)

    Lv, Qiming; Schneider, Manuel K; Pitchford, Jonathan W

    2008-08-01

    We study individual plant growth and size hierarchy formation in an experimental population of Arabidopsis thaliana, within an integrated analysis that explicitly accounts for size-dependent growth, size- and space-dependent competition, and environmental stochasticity. It is shown that a Gompertz-type stochastic differential equation (SDE) model, involving asymmetric competition kernels and a stochastic term which decreases with the logarithm of plant weight, efficiently describes individual plant growth, competition, and variability in the studied population. The model is evaluated within a Bayesian framework and compared to its deterministic counterpart, and to several simplified stochastic models, using distributional validation. We show that stochasticity is an important determinant of size hierarchy and that SDE models outperform the deterministic model if and only if structural components of competition (asymmetry; size- and space-dependence) are accounted for. Implications of these results are discussed in the context of plant ecology and in more general modelling situations.

  2. Cell Differentiation in a Bacillus thuringiensis Population during Planktonic Growth, Biofilm Formation, and Host Infection.

    Science.gov (United States)

    Verplaetse, Emilie; Slamti, Leyla; Gohar, Michel; Lereclus, Didier

    2015-04-28

    Bacillus thuringiensis (Bt) is armed to complete a full cycle in its insect host. During infection, virulence factors are expressed under the control of the quorum sensor PlcR to kill the host. After the host's death, the quorum sensor NprR controls a necrotrophic lifestyle, allowing the vegetative cells to use the insect cadaver as a bioincubator and to survive. Only a part of the Bt population sporulates in the insect cadaver, and the precise composition of the whole population and its evolution over time are unknown. Using fluorescent reporters to record gene expression at the single-cell level, we have determined the differentiation course of a Bt population and explored the lineage existing among virulent, necrotrophic, and sporulating cells. The dynamics of cell differentiation were monitored during growth in homogenized medium, biofilm formation, and colonization of insect larvae. We demonstrated that in the insect host and in planktonic culture in rich medium, the virulence, necrotrophism, and sporulation regulators are successively activated in the same cell. In contrast, in biofilms, activation of PlcR is dispensable for NprR activation and we observed a greater heterogeneity than under the other two growth conditions. We also showed that sporulating cells arise almost exclusively from necrotrophic cells. In biofilm and in the insect cadaver, we identified an as-yet-uncharacterized category of cells that do not express any of the reporters used. Overall, we showed that PlcR, NprR, and Spo0A act as interconnected integrators to allow finely tuned adaptation of the pathogen to its environment. Bt is an entomopathogen found ubiquitously in the environment and is a widely used biopesticide. Studies performed at the population level suggest that the infection process of Bt includes three successive steps (virulence, necrotrophism, and sporulation) controlled by different regulators. This study aimed to determine how these phenotypes are activated at the

  3. The genetic basis of adaptive population differentiation: A quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Vanhala, T.K.; Biere, A.; Nevo, E.; Damme, van J.M.M.

    2004-01-01

    We used a quantitative trait locus (QTL) approach to study the genetic basis of population differentiation in wild barley, Hordeum spontaneum. Several ecotypes are recognized in this model species, and population genetic studies and reciprocal transplant experiments have indicated the role of local

  4. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2010-01-01

    We consider dynamic congestion in an urban setting where trip origins are spatially distributed. All travelers must pass through a downtown bottleneck in order to reach their destination in the CBD. Each traveler chooses departure time to maximize general concave scheduling utility. At equilibriu...

  5. In Quest of the Bottleneck - Monitoring Parallel Database Systems

    NARCIS (Netherlands)

    S. Manegold (Stefan); F. Waas; D. Gudlat

    1997-01-01

    textabstractMonitoring query processing has proven to be an effective technique to detect bottlenecks in sequential query execution systems' components. Monitoring distributed execution in parallel systems, however, is a difficult task. The monitoring data of all nodes must be collected at the same

  6. Bottlenecks reduction using superconductors in high voltage transmission lines

    Directory of Open Access Journals (Sweden)

    Daloub Labib

    2016-01-01

    Full Text Available Energy flow bottlenecks in high voltage transmission lines known as congestions are one of the challenges facing power utilities in fast developing countries. Bottlenecks occur in selected power lines when transmission systems are operated at or beyond their transfer limits. In these cases, congestions result in preventing new power supply contracts, infeasibility in existing contracts, price spike and market power abuse. The “Superconductor Technology” in electric power transmission cables has been used as a solution to solve the problem of bottlenecks in energy transmission at high voltage underground cables and overhead lines. The increase in demand on power generation and transmission happening due to fast development and linked to the intensive usage of transmission network in certain points, which in turn, lead to often frequent congestion in getting the required power across to where it is needed. In this paper, a bottleneck in high voltage double overhead transmission line with Aluminum Conductor Steel Reinforced was modeled using conductor parameters and replaced by Gap-Type Superconductor to assess the benefit of upgrading to higher temperature superconductor and obtain higher current carrying capacity. This proved to reduce the high loading of traditional aluminum conductors and allow more power transfer over the line using superconductor within the same existing right-of-way, steel towers, insulators and fittings, thus reducing the upgrade cost of building new lines.

  7. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2012-01-01

    We consider dynamic congestion in an urban setting where trip origins are spatially distributed. All travelers must pass through a downtown bottleneck in order to reach their destination in the CBD. Each traveler chooses departure time to maximize general concave scheduling utility. We find that,...

  8. The bottleneck may be the solution, not the problem.

    Science.gov (United States)

    Lotem, Arnon; Kolodny, Oren; Halpern, Joseph Y; Onnis, Luca; Edelman, Shimon

    2016-01-01

    As a highly consequential biological trait, a memory "bottleneck" cannot escape selection pressures. It must therefore co-evolve with other cognitive mechanisms rather than act as an independent constraint. Recent theory and an implemented model of language acquisition suggest that a limit on working memory may evolve to help learning. Furthermore, it need not hamper the use of language for communication.

  9. Assessment of demographic bottleneck in Indian horse and ...

    Indian Academy of Sciences (India)

    2National Bureau of Animal Genetic Resource, Karnal 132 001, India. [Gupta A. K., Chauhan M., Bhardwaj A. and Vijh R. K. 2015 Assessment of demographic bottleneck in Indian horse and endangered pony breeds. J. Genet. 94, e56–e62. Online only: http://www.ias.ac.in/jgenet/OnlineResources/94/e56.pdf]. Introduction.

  10. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 ...

  11. IGF1 stimulates crypt expansion via differential activation of 2 intestinal stem cell populations

    Science.gov (United States)

    Van Landeghem, Laurianne; Santoro, M. Agostina; Mah, Amanda T.; Krebs, Adrienne E.; Dehmer, Jeffrey J.; McNaughton, Kirk K.; Helmrath, Michael A.; Magness, Scott T.; Lund, P. Kay

    2015-01-01

    Insulin-like growth factor 1 (IGF1) has potent trophic effects on normal or injured intestinal epithelium, but specific effects on intestinal stem cells (ISCs) are undefined. We used Sox9-enhanced green fluorescent protein (EGFP) reporter mice that permit analyses of both actively cycling ISCs (Sox9-EGFPLow) and reserve/facultative ISCs (Sox9-EGFPHigh) to study IGF1 action on ISCs in normal intestine or during crypt regeneration after high-dose radiation-induced injury. We hypothesized that IGF1 differentially regulates proliferation and gene expression in actively cycling and reserve/facultative ISCs. IGF1 was delivered for 5 days using subcutaneously implanted mini-pumps in uninjured mice or after 14 Gy abdominal radiation. ISC numbers, proliferation, and transcriptome were assessed. IGF1 increased epithelial growth in nonirradiated mice and enhanced crypt regeneration after radiation. In uninjured and regenerating intestines, IGF1 increased total numbers of Sox9-EGFPLow ISCs and percentage of these cells in M-phase. IGF1 increased percentages of Sox9-EGFPHigh ISCs in S-phase but did not expand this population. Microarray revealed that IGF1 activated distinct gene expression signatures in the 2 Sox9-EGFP ISC populations. In vitro IGF1 enhanced enteroid formation by Sox9-EGFPHigh facultative ISCs but not Sox9-EGFPLow actively cycling ISCs. Our data provide new evidence that IGF1 activates 2 ISC populations via distinct regulatory pathways to promote growth of normal intestinal epithelium and crypt regeneration after irradiation.—Van Landeghem, L., Santoro, M. A., Mah, A. T., Krebs, A. E., Dehmer, J. J., McNaughton, K. K., Helmrath, M. A., Magness, S. T., Lund, P. K. IGF1 stimulates crypt expansion via differential activation of 2 intestinal stem cell populations. PMID:25837582

  12. Numerical rate function determination in partial differential equations modeling cell population dynamics.

    Science.gov (United States)

    Groh, Andreas; Kohr, Holger; Louis, Alfred K

    2017-02-01

    This paper introduces a method to solve the inverse problem of determining an unknown rate function in a partial differential equation (PDE) based on discrete measurements of the modeled quantity. The focus is put on a size-structured population balance equation (PBE) predicting the evolution of the number distribution of a single cell population as a function of the size variable. Since the inverse problem at hand is ill-posed, an adequate regularization scheme is required to avoid amplification of measurement errors in the solution method. The technique developed in this work to determine a rate function in a PBE is based on the approximate inverse method, a pointwise regularization scheme, which employs two key ideas. Firstly, the mollification in the directions of time and size variables are separated. Secondly, instable numerical data derivatives are circumvented by shifting the differentiation to an analytically given function. To examine the performance of the introduced scheme, adapted test scenarios have been designed with different levels of data disturbance simulating the model and measurement errors in practice. The success of the method is substantiated by visualizing the results of these numerical experiments.

  13. Habitat continuity and geographic distance predict population genetic differentiation in giant kelp.

    Science.gov (United States)

    Alberto, Filipe; Raimondi, Peter T; Reed, Daniel C; Coelho, Nelson C; Leblois, Raphael; Whitmer, Allison; Serrão, Ester A

    2010-01-01

    Isolation by distance (IBD) models are widely used to predict levels of genetic connectivity as a function of Euclidean distance, and although recent studies have used GIS-landscape ecological approaches to improve the predictability of spatial genetic structure, few if any have addressed the effect of habitat continuity on gene flow. Landscape effects on genetic connectivity are even less understood in marine populations, where habitat mapping is particularly challenging. In this study, we model spatial genetic structure of a habitat-structuring species, the giant kelp Macrocystis pyrifera, using highly variable microsatellite markers. GIS mapping was used to characterize habitat continuity and distance between sampling sites along the mainland coast of the Santa Barbara Channel, and their roles as predictors of genetic differentiation were evaluated. Mean dispersal distance (sigma) and effective population size (Ne) were estimated by comparing our IBD slope with those from simulations incorporating habitat continuity and spore dispersal characteristics of the study area. We found an allelic richness of 7-50 alleles/locus, which to our knowledge is the highest reported for macroalgae. The best regression model relating genetic distance to habitat variables included both geographic distance and habitat continuity, which were respectively, positively and negatively related to genetic distance. Our results provide strong support for a dependence of gene flow on both distance and habitat continuity and elucidate the combination of Ne and a that explained genetic differentiation.

  14. Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape.

    Science.gov (United States)

    Kekkonen, J; Seppä, P; Hanski, I K; Jensen, H; Väisänen, R A; Brommer, J E

    2011-01-01

    The house sparrow Passer domesticus has been declining in abundance in many localities, including Finland. We studied the genetic diversity and differentiation of the house sparrow populations across Finland in the 1980s, at the onset of the species' decline in abundance. We genotyped 472 adult males (the less dispersive sex) from 13 locations in Finland (covering a range of 400 × 800 km) and one in Sweden (Stockholm) for 13 polymorphic microsatellite markers. Our analysis of Finnish ringing records showed that natal dispersal distances are limited (90% genetically very homogeneous and the limited dispersal was sufficiently large to maintain their connectivity. However, all Finnish populations differed significantly from the Stockholm population, even though direct geographical distance to it was often smaller than among Finnish populations. Hence, the open sea between Finland and Sweden appears to form a dispersal barrier for this species, whereas dispersal is much less constrained across the Finnish mainland (which lacks geographical barriers). Our findings provide a benchmark for conservation biologists and emphasize the influence of landscape structure on gene flow.

  15. Approximate reduction of linear population models governed by stochastic differential equations: application to multiregional models.

    Science.gov (United States)

    Sanz, Luis; Alonso, Juan Antonio

    2017-12-01

    In this work we develop approximate aggregation techniques in the context of slow-fast linear population models governed by stochastic differential equations and apply the results to the treatment of populations with spatial heterogeneity. Approximate aggregation techniques allow one to transform a complex system involving many coupled variables and in which there are processes with different time scales, by a simpler reduced model with a fewer number of 'global' variables, in such a way that the dynamics of the former can be approximated by that of the latter. In our model we contemplate a linear fast deterministic process together with a linear slow process in which the parameters are affected by additive noise, and give conditions for the solutions corresponding to positive initial conditions to remain positive for all times. By letting the fast process reach equilibrium we build a reduced system with a lesser number of variables, and provide results relating the asymptotic behaviour of the first- and second-order moments of the population vector for the original and the reduced system. The general technique is illustrated by analysing a multiregional stochastic system in which dispersal is deterministic and the rate growth of the populations in each patch is affected by additive noise.

  16. Morphological heterogeneity and population differentiation in the green chromid Etroplus suratensis (Pisces: Cichlidae in Sri Lanka

    Directory of Open Access Journals (Sweden)

    K. B. Suneetha Gunawickrama

    2007-09-01

    Full Text Available Morphological variation of the euryhaline cichlid fish Etroplus suratensis (Bloch from six geographically apart estuarine localities along the southern and western coasts of Sri Lanka was studied. Significant heterogeneity in morphology of the cichlid were found with respect to nine morphometric characters (n=218. Fish of Nilwala estuary and Garanduwa lagoon were not significantly different in morphology, yet they show discernible differences from the other four samples (Kahanda lagoon, Chilaw lagoon, Walawe estuary and Koggala lagoon with respect to the most of the studied characters. Concordant results were found by multivariate analysis of the sizecorrected morphological data as well. Three functions were significant in discriminating the populations of which the first two functions accounted for 95% of the covariance (CV1 85.4 % and CV2 9.7%. The function with the greatest discriminatory power (CV1 can clearly separate samples of Nilwala estuary (L5 and Garanduwa lagoon (L6 from the rest of the samples, while the magnitude of the discrimination between the latter samples is much smaller. Classification functions could correctly classify an average of 65.7% of the individuals into their respective a priori population units. No evidence was found for isolation-by-distance model. The results suggest that E. suratensis populations in some of the studied estuarine localities maintain significant morphological heterogeneity, and the morphological variation can be used to differentiate some of these populations.

  17. Life history trait differentiation and local adaptation in invasive populations of Ambrosia artemisiifolia in China.

    Science.gov (United States)

    Li, Xiao-Meng; She, Deng-Ying; Zhang, Da-Yong; Liao, Wan-Jin

    2015-03-01

    Local adaptation has been suggested to play an important role in range expansion, particularly among invasive species. However, the extent to which local adaptation affects the success of an invasive species and the factors that contribute to local adaptation are still unclear. This study aimed to investigate a case of population divergence that may have contributed to the local adaptation of invasive populations of Ambrosia artemisiifolia in China. Common garden experiments in seven populations indicated clinal variations along latitudinal gradients, with plants from higher latitudes exhibiting earlier flowering and smaller sizes at flowering. In reciprocal transplant experiments, plants of a northern Beijing origin produced more seeds at their home site than plants of a southern Wuhan origin, and the Wuhan-origin plants had grown taller at flowering than the Beijing-origin plants in Wuhan, which is believed to facilitate pollen dispersal. These results suggest that plants of Beijing origin may be locally adapted through female fitness and plants from Wuhan possibly locally adapted through male fitness. Selection and path analysis suggested that the phenological and growth traits of both populations have been influenced by natural selection and that flowering time has played an important role through its direct and indirect effects on the relative fitness of each individual. This study evidences the life history trait differentiation and local adaptation during range expansion of invasive A. artemisiifolia in China.

  18. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system.

    Directory of Open Access Journals (Sweden)

    Ganeshprasad Arunkumar

    Full Text Available Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined with a shared genetic heritage dating back to the late Pleistocene (10-30 Kya, suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4-6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.

  19. Microsatellite DNA analysis of northern pike ( Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

    DEFF Research Database (Denmark)

    Jacobsen, B. H.; Hansen, Michael Møller; Loeschcke, V.

    2005-01-01

    low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations...... product of effective population size and mutation rate) among populations from large and small water bodies, but the relative differences in theta were smaller than expected, which could reflect population subdivision within the larger water bodies. Finally, the analyses showed drastic population declines...... on a time scale of several thousand years within European populations, which we ascribe to either glacial bottlenecks or postglacial founder events. (C) 2005 The Linnean Society of London....

  20. Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans.

    Science.gov (United States)

    Ceh, E; Dovc, P

    2014-08-01

    Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on FST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour-joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed

  1. Differential Impact of Tobacco Control Policies on Youth Sub-Populations

    Directory of Open Access Journals (Sweden)

    John A. Tauras

    2013-09-01

    Full Text Available Background: While previous studies have demonstrated the efficacy of tobacco control interventions in reducing tobacco use among youth overall, there have been very few studies that examine the potential differential impact of tobacco control policies on various youth subgroups, defined by socio-economic status (SES, race/ethnicity, and gender. Objective: We examined the relationship between state-level cigarette prices and smoke-free air laws and youth smoking prevalence and intensity for various youth sub-populations in the United States. Methods: We estimated a 2-part model of cigarette demand using data from the 1991 through 2010 nationally representative surveys of 8th-, 10th-, and 12th-grade students as part of the Monitoring the Future project. Findings: We found that real cigarette prices are strong determinants of youth smoking. Blacks, females, Hispanics, and low-SES subpopulations are found to have a larger price response with respect to smoking prevalence than the full sample. Smoke-free air laws are found to have a negative effect on smoking prevalence for the full sample and for the male, white, and high-SES sub-populations. Conclusions: This research concludes that higher cigarette prices will reduce smoking prevalence rates of Blacks, Hispanics, females, and low-SES subpopulations faster than the overall youth population and other youth sub-populations. Moreover, this research concludes that smoke-free air laws will reduce smoking prevalence for the overall youth population with the largest reductions in high SES and male subpopulations.

  2. Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments.

    Science.gov (United States)

    Donohue, K; Pyle, E H; Messiqua, D; Heschel, M S; Schmitt, J

    2000-12-01

    We identified environment-dependent constraints on the evolution of plasticity to density under natural conditions in two natural populations of Impatiens capensis. We also examined the expression of population divergence in genetic variance-covariance matrices in these natural environments. Inbred lines, originally collected from a sunny site with high seedling densities and a woodland site with low seedling densities, were planted in both original sites at natural high densities and at low density. Morphological and life-history characters were measured. More genetic variation for plastic responses to density was expressed in the sun site than in the woodland site, so the evolutionary potential of plasticity was greater in the sun site. Strong genetic correlations between the same character expressed at different densities and correlations among different characters could constrain the evolution of plasticity in both sites. Genetically based trade-offs in meristem allocation to vegetative growth and reproduction were apparent only in the high-resource environment with no overhead canopy and no intraspecific competition. Therefore, genetic constraints on the evolution of plasticity depended on the site and density in which plants were grown, and correlated responses to selection on plastic characters are also expected to differ between sites and densities. Population differentiation in genetic variance-covariance matrices was detected, but matrix structural differences, as opposed to proportional differences, were detected between populations only in the sun site at natural high density. Thus, population divergence in genetic architecture can occur rapidly and on a fine spatial scale, but the expression of such divergence may depend on the environment.

  3. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear.

    Science.gov (United States)

    Xenikoudakis, G; Ersmark, E; Tison, J-L; Waits, L; Kindberg, J; Swenson, J E; Dalén, L

    2015-07-01

    The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution. © 2015 John Wiley & Sons Ltd.

  4. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.

    Science.gov (United States)

    Marsden, Clare D; Ortega-Del Vecchyo, Diego; O'Brien, Dennis P; Taylor, Jeremy F; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D; Wayne, Robert K; Lohmueller, Kirk E

    2016-01-05

    Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

  5. Woody climbers show greater population genetic differentiation than trees: Insights into the link between ecological traits and diversification.

    Science.gov (United States)

    Gianoli, Ernesto; Torres-Díaz, Cristian; Ruiz, Eduardo; Salgado-Luarte, Cristian; Molina-Montenegro, Marco A; Saldaña, Alfredo; Ríos, Rodrigo S

    2016-12-01

    The climbing habit is a key innovation in plants: climbing taxa have higher species richness than nonclimbing sister groups. We evaluated the hypothesis that climbing plant species show greater among-population genetic differentiation than nonclimber species. We compared the among-population genetic distance in woody climbers (eight species, 30 populations) and trees (seven species, 29 populations) coexisting in nine communities in a temperate rainforest. We also compared within-population genetic diversity in co-occurring woody climbers and trees in two communities. Mean genetic distance between populations of climbers was twice that of trees. Isolation by distance (increase in genetic distance with geographic distance) was greater for climbers. Climbers and trees showed similar within-population genetic diversity. Our longevity estimate suggested that climbers had shorter generation times, while other biological features often associated with diversification (dispersal and pollination syndromes, mating system, size, and metabolic rate) did not show significant differences between groups. We hypothesize that the greater population differentiation in climbers could result from greater evolutionary responses to local selection acting on initially higher within-population genetic diversity, which could be driven by neutral processes associated with shorter generation times. Increased population genetic differentiation could be incorporated as another line of evidence when testing for key innovations. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  6. Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation.

    Science.gov (United States)

    Nyakaana, Silvester; Stothard, J Russell; Nalugwa, Allen; Webster, Bonnie L; Lange, Charles N; Jørgensen, Aslak; Rollinson, David; Kristensen, Thomas K

    2013-11-01

    Bulinus globosus, a key intermediate host for Schistosoma haematobium that causes urinary schistosomiasis, is a hermaphroditic freshwater Planorbid snail species that inhabits patchy and transient water bodies prone to large seasonal variations in water availability. Although capable of self-fertilizing, this species has been reported to be preferentially out crossing. In this study, we characterized the population genetic structure of 19 B. globosus populations sampled across the Lake Victoria basin and coastal Kenya using four polymorphic microsatellite loci. Population genetic structure was characterized and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging from 16 to 22. Average observed and expected heterozygosities across loci in each population ranged from 0.13 to 0.69 and from 0.39 to 0.79, respectively. Twenty-five of the seventy-six possible population-locus comparisons significantly deviated from Hardy-Weinberg equilibrium proportions after Bonferroni corrections, mostly due to the deficiency of heterozygotes. Significant genetic differentiation was observed between populations and Bayesian inferences identified 15 genetic clusters. The excess homozygosity, significant inbreeding and population genetic differentiation observed in B. globosus populations are likely to be due to the habitat patchiness, mating system and the proneness to cyclic extinction and recolonization in transient habitats. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Patterns of genetic and reproductive traits differentiation in Mainland vs. Corsican populations of bumblebees

    National Research Council Canada - National Science Library

    Lecocq, Thomas; Vereecken, Nicolas J; Michez, Denis; Dellicour, Simon; Lhomme, Patrick; Valterová, Irena; Rasplus, Jean-Yves; Rasmont, Pierre

    2013-01-01

    .... While phenotypic differentiation in characters, such as size or shape among insular organisms, has been well studied, insular differentiation in quantitative reproductive traits involved in chemical...

  8. Endothelial Progenitor Cell Fraction Contained in Bone Marrow-Derived Mesenchymal Stem Cell Populations Impairs Osteogenic Differentiation

    Directory of Open Access Journals (Sweden)

    Fabian Duttenhoefer

    2015-01-01

    Full Text Available In bone tissue engineering (TE endothelial cell-osteoblast cocultures are known to induce synergies of cell differentiation and activity. Bone marrow mononucleated cells (BMCs are a rich source of mesenchymal stem cells (MSCs able to develop an osteogenic phenotype. Endothelial progenitor cells (EPCs are also present within BMC. In this study we investigate the effect of EPCs present in the BMC population on MSCs osteogenic differentiation. Human BMCs were isolated and separated into two populations. The MSC population was selected through plastic adhesion capacity. EPCs (CD34+ and CD133+ were removed from the BMC population and the resulting population was named depleted MSCs. Both populations were cultured over 28 days in osteogenic medium (Dex+ or medium containing platelet lysate (PL. MSC population grew faster than depleted MSCs in both media, and PL containing medium accelerated the proliferation for both populations. Cell differentiation was much higher in Dex+ medium in both cases. Real-time RT-PCR revealed upregulation of osteogenic marker genes in depleted MSCs. Higher values of ALP activity and matrix mineralization analyses confirmed these results. Our study advocates that absence of EPCs in the MSC population enables higher osteogenic gene expression and matrix mineralization and therefore may lead to advanced bone neoformation necessary for TE constructs.

  9. Linguistics, cognitive psychology, and the Now-or-Never bottleneck.

    Science.gov (United States)

    Endress, Ansgar D; Katzir, Roni

    2016-01-01

    Christiansen & Chater (C&C)'s key premise is that "if linguistic information is not processed rapidly, that information is lost for good" (sect. 1, para. 1). From this "Now-or-Never bottleneck" (NNB), C&C derive "wide-reaching and fundamental implications for language processing, acquisition and change as well as for the structure of language itself" (sect. 2, para. 10). We question both the premise and the consequentiality of its purported implications.

  10. Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes

    OpenAIRE

    Monsees, Hendrik; Kloas, Werner; Wuertz, Sven

    2017-01-01

    In classical aquaponics (coupled aquaponic systems, 1-loop systems) the production of fish in recirculating aquaculture systems (RAS) and plants in hydroponics are combined in a single loop, entailing systemic compromises on the optimal production parameters (e.g. pH). Recently presented decoupled aquaponics (2-loop systems) have been awarded for eliminating major bottlenecks. In a pilot study, production in an innovative decoupled aquaponic system was compared with a coupled system and, as a...

  11. The problem state: a cognitive bottleneck in multitasking.

    Science.gov (United States)

    Borst, Jelmer P; Taatgen, Niels A; van Rijn, Hedderik

    2010-03-01

    The main challenge for theories of multitasking is to predict when and how tasks interfere. Here, we focus on interference related to the problem state, a directly accessible intermediate representation of the current state of a task. On the basis of Salvucci and Taatgen's (2008) threaded cognition theory, we predict interference if 2 or more tasks require a problem state but not when only one task requires one. This prediction was tested in a series of 3 experiments. In Experiment 1, a subtraction task and a text entry task had to be carried out concurrently. Both tasks were presented in 2 versions: one that required maintaining a problem state and one that did not. A significant overadditive interaction effect was observed, showing that the interference between tasks was maximal when both tasks required a problem state. The other 2 experiments tested whether the interference was indeed due to a problem state bottleneck, instead of cognitive load (Experiment 2: an alternative subtraction and text entry experiment) or a phonological loop bottleneck (Experiment 3: a triple-task experiment that added phonological processing). Both experiments supported the problem state hypothesis. To account for the observed behavior, computational cognitive models were developed using threaded cognition within the context of the cognitive architecture ACT-R (Anderson, 2007). The models confirm that a problem state bottleneck can explain the observed interference.

  12. Allozyme variation in Pinus cembra and P. sibirica: differentiation between populations and species

    Directory of Open Access Journals (Sweden)

    D.V. Politov

    2013-12-01

    Full Text Available Two closely related Eurasian species of 5-needle pines, Swiss stone pine(Pinus cembra L. and Siberian stone pine (P. sibirica Du Tour occupy two disjunctive parts of the formerly common range in Europe andSiberia, respectively. These forms show so close morphological and genetic similarity that in some classifications they are treated as subspecies. Using a set of 29 allozyme loci (Adh-1,-2, Fdh, Fest-2, Gdh, Got-1,-2,-3, Idh, Lap- 2,-3, Mdh-1,-2,-3,-4, Mnr-1, Pepca, 6-Pgd-1,-2,-3, Pgi-1,-2, Pgm-1,-2, Skdh-1,-2, Sod-2,-3,- 4 we analyzed genetic differentiation within the Alpine-Carpathian part of the range (P.cembra and found relatively low genetic diversity for conifers (HE=0,08 and moderate level of differentiation (FST=7,4%. For thesame loci set within Siberian populations (P. sibirica genic diversity was higher (0,14, while differentiation was lower (3%. The factthat differentiation within the highly fragmented range of Swiss stone pine is just 2.5 times higher than in widespread closely related P.sibirica makes us consider factors other than unlimited gene flow responsible for uniformity of allelic frequencies. Among these factors the leading role belongs to balancing selection.Heterozygote superiority leads to both (i increasing of heterozygosity in course of stand development and (ii through balancing selectionto stable equilibrium state. Under this equilibrium, virtually the same genetic structure is maintained, even when remote and isolatedparts of the species' ranges are compared. For many studied loci, Swiss and Siberian stone pines have the same allelic profiles despite the fact that gene flow among them ceased a long time ago. According to one point of view fragmentation of the formerly united range might take place in the Atlantic time of the Holocene (about 5000 years BC, however, an alternative hypothesis refers to a much earlierPleistocene glacial time. Analysis of a combined data set (P. cembra

  13. Differentiating medicinal from illicit use in positive methamphetamine results in a pain population.

    Science.gov (United States)

    West, Robert; Pesce, Amadeo; West, Cameron; Mikel, Charles; Velasco, Javier; Gonzales, Elizabeth; Dizon, Zenaida; Almazan, Perla; Latyshev, Sergey

    2013-03-01

    In addition to illicit methamphetamine, there are prescription and over-the-counter medications that, if ingested, may yield positive methamphetamine (MAMP) results on laboratory urine drug tests. The purpose of the study is to estimate the prevalence of medicinal and illicit MAMP in the pain population using chiral analysis to determine the relative amounts of the d and l-MAMP enantiomers. This retrospective analysis included the LC-MS/MS results and prescriber provided medication histories of 485,889 de-identified urine specimens from patients treated for pain. Two groups of 100 specimens each were subjected to chiral analysis. Group 1 contained specimens that were MAMP positive and amphetamine negative. Group 2 contained randomly selected MAMP positive specimens. The overall MAMP positivity rate of the 485,889 specimens tested was 1.6%. The prevalence of MAMP medications based on reported medications and detection of l-MAMP in Group 1 and Group 2 was 44% and 6%, respectively. These data indicate that the use of both illicit and medicinal MAMP is found in this patient population, and that medicinal use is underreported in clinical histories. Therefore, clinical laboratories should provide on request chiral analysis to aid in differentiating illicit and medicinal MAMP.

  14. Statistical guidelines for detecting past population shifts using ancient DNA

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon Y. W.; Gilbert, Tom

    2012-01-01

    post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our...... based solely on mitochondrial information....

  15. Adaptive genetic variability and differentiation of Croatian and Austrian Quercus robur L. populations at a drought prone field trial

    Directory of Open Access Journals (Sweden)

    Saša Bogdan

    2017-07-01

    Full Text Available Provenance trials, where populations of different geographical origin are tested in a common environment (common garden test, are a tool suited to allow the study of intraspecific adaptive genetic variation. Research of pedunculate oak (Quercus robur L. adaptive genetic variability through analyses of populations in common garden tests has a long tradition. However, pedunculated oak populations originating south-eastern from the Alps have been scarcely studied in this way. This study addresses the adaptive genetic variability and differentiation of pedunculate oak populations originating from Austria and Croatia in a provenance/progeny field trial. Studied plants were six years old and were growing at the trial for three years. After two years of unusually low precipitations height and survival were analysed. The total mean height of all plants in the trial was 137.8 cm and ranged from 123.0 cm to 151.8 cm. The overall mean survival rate was rather high (0.85. Mean population survival ranged from 0.64 to 0.94. Individual narrow-sense heritabilities (hi2, family mean heritabilities (hf2, the coefficients of additive genetic variation (CVA and quantitative genetic differentiation coefficients (QST were calculated. A multivariate regression tree (MRT analysis was used to determine the pattern of genetic differentiation of the populations. Individual heritabilities for height ranged between 0.00 and 0.39. Family mean heritabilities for height were rather low in most populations as well (<0.5. Family mean heritabilities for survival were higher than for height (ranging between 0.00 and 0.77. Calculated QST coefficients (0.25 for height and 0.14 for survival indicated between-population genetic differentiation. The populations were separated into two clusters by MRT analysis regarding a climatic variable, namely Hargreaves’ reference evapotranspiration. Populations originating from comparatively more humid habitats were grouped in the first

  16. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.).

    Science.gov (United States)

    Sim, S-C; Robbins, M D; Van Deynze, A; Michel, A P; Francis, D M

    2011-06-01

    Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise F(st) (θ) and Nei's standard genetic distance. We also identified a total of 19 loci under positive selection between processing, fresh-market and vintage germplasm by using an F(st)-outlier method based on the deviation from the expected distribution of F(st) and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato.

  17. Phenotypic differentiation of the Solidago virgaurea complex along an elevational gradient: Insights from a common garden experiment and population genetics.

    Science.gov (United States)

    Hirano, Masaaki; Sakaguchi, Shota; Takahashi, Koichi

    2017-09-01

    Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations. Leaf mass per area was lower, while leaf nitrogen and chlorophyll concentrations were greater for higher elevations at which seeds were originally collected. For reproductive traits, plants derived from higher elevations had larger flower heads on shorter stems and flowering started earlier. These elevational changes in morphology were consistent with the clines in the field, indicating that phenotypic variation along the elevational gradient would have been caused by genetic differentiation. However, population genetic analysis using 16 microsatellite loci suggested an extremely low level of genetic differentiation of neutral genes among the nine populations. Analysis of molecular variance also indicated that most genetic variation was partitioned into individuals within a population, and the genetic differentiation among the populations was not significant. This study suggests that genome regions responsible for adaptive traits may differ among the populations despite the existence of gene flow and that phenotypic variation of the S. virgaurea complex along the elevational gradient is maintained by strong selection pressure.

  18. Gene variation and genetic differentiation among populations of the solitary mud dauber wasp Trypoxylon (Trypargilum albitarse Fabricius 1804 (Hymenoptera, Crabronidae

    Directory of Open Access Journals (Sweden)

    Antonio C.B. Bergamaschi

    2015-01-01

    Full Text Available Abstract Trypoxylon is a genus of solitary crabronid wasps whose population genetics is poorly known. The purpose of the present study was to investigate the genetic variation and differentiation among five populations of Trypoxylon albitarse, a species widely distributed throughout the Neotropics, with records from Panama to northern Argentina. Eight species-specific microsatellite loci were used for genotyping 96 adult wasps (one female per nest sampled at five sites in Brazil. The analysis of allelic richness and private alleles indicated high genetic diversity in the populations sampled. Pairwise comparisons using the Fst and Dest indices revealed significant differentiation for all, but one pair of populations. Fst, Dest, AMOVA and assignment test values pointed to inter-population differentiation. Additionally, the analysis of population structure using Bayesian and PCA methods characterized two alternative genetic groups. The Mantel test indicated no correlation between genetic and geographic distances. Despite evidence of considerable dispersal capacity for T. albitarse, the data indicate low to moderate population structuring in this species.

  19. Platelet activation patterns in platelet size sub-populations: differential responses to aspirin in vitro.

    Science.gov (United States)

    Mangalpally, Kiran Kumar R; Siqueiros-Garcia, Alan; Vaduganathan, Muthiah; Dong, Jing-Fei; Kleiman, Neal S; Guthikonda, Sasidhar

    2010-10-01

    Circulating platelets are heterogeneous in size and structure. Whether this translates into differences in platelet function and efficacy of antiplatelet therapy is unclear. Hence, we decided to investigate the activation patterns among different platelet populations differentiated by size, and to compare the inhibitory effects of aspirin in these populations. Circulating platelets from 9 healthy volunteers were separated by size and stratified into the largest and smallest quintiles. Platelets were stimulated with 75 μM arachidonic acid (AA), 10 μM ADP or 25 μM TRAP. Alpha-granule protein secretion and expression (P-selectin, VWF, fibrinogen), surface-protein activation (activated integrin αIIbβ3) were assessed. Platelet thromboxane B(2) (TxB(2)) synthesis following AA stimulation was measured in vitro before and after incubation with 265 μM aspirin. Reticulated (juvenile) platelets were assessed using thiazole orange staining. A greater number of large platelets in the largest quintile were reticulated compared with the smallest quintile (6.1 ± 2.8% vs. 1.2 ± 1.5% respectively, p aspirin (1029 ± 190 pg/mL vs. 851 ± 159 pg/mL, respectively, p = 0.03). After stimulation with each agonist, a greater proportion of large platelets bound fibrinogen, VWF, P-selectin and activated integrin αIIbβ3 than small platelets both in the presence and in the absence of in vitro aspirin. In an in vitro setting, large platelets appear to be more active than small platelets and continue to be more active even after in vitro aspirin. Platelets exhibit heterogeneity in size and structure. Whether this translates into platelet function and efficacy of antiplatelet therapy is unclear. We evaluated platelet functional properties and the effects of aspirin on separated platelet subpopulations in an in vitro setting. Platelets were sorted into the largest and smallest size quintiles using flow cytometry forward scatter. Alpha-granule protein release, dense granule content

  20. Latent variable mixture models to test for differential item functioning: a population-based analysis.

    Science.gov (United States)

    Wu, Xiuyun; Sawatzky, Richard; Hopman, Wilma; Mayo, Nancy; Sajobi, Tolulope T; Liu, Juxin; Prior, Jerilynn; Papaioannou, Alexandra; Josse, Robert G; Towheed, Tanveer; Davison, K Shawn; Lix, Lisa M

    2017-05-15

    Comparisons of population health status using self-report measures such as the SF-36 rest on the assumption that the measured items have a common interpretation across sub-groups. However, self-report measures may be sensitive to differential item functioning (DIF), which occurs when sub-groups with the same underlying health status have a different probability of item response. This study tested for DIF on the SF-36 physical functioning (PF) and mental health (MH) sub-scales in population-based data using latent variable mixture models (LVMMs). Data were from the Canadian Multicentre Osteoporosis Study (CaMos), a prospective national cohort study. LVMMs were applied to the ten PF and five MH SF-36 items. A standard two-parameter graded response model with one latent class was compared to multi-class LVMMs. Multivariable logistic regression models with pseudo-class random draws characterized the latent classes on demographic and health variables. The CaMos cohort consisted of 9423 respondents. A three-class LVMM fit the PF sub-scale, with class proportions of 0.59, 0.24, and 0.17. For the MH sub-scale, a two-class model fit the data, with class proportions of 0.69 and 0.31. For PF items, the probabilities of reporting greater limitations were consistently higher in classes 2 and 3 than class 1. For MH items, respondents in class 2 reported more health problems than in class 1. Differences in item thresholds and factor loadings between one-class and multi-class models were observed for both sub-scales. Demographic and health variables were associated with class membership. This study revealed DIF in population-based SF-36 data; the results suggest that PF and MH sub-scale scores may not be comparable across sub-groups defined by demographic and health status variables, although effects were frequently small to moderate in size. Evaluation of DIF should be a routine step when analysing population-based self-report data to ensure valid comparisons amongst sub-groups.

  1. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Directory of Open Access Journals (Sweden)

    Katrin Kuhls

    2008-07-01

    Full Text Available Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1.We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1 Greece; (2 Spain islands-Majorca/Ibiza; (3 mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles.In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological investigations.

  2. The Plasmodium bottleneck: malaria parasite losses in the mosquito vector

    Science.gov (United States)

    Smith, Ryan C; Vega-Rodríguez, Joel; Jacobs-Lorena, Marcelo

    2014-01-01

    Nearly one million people are killed every year by the malaria parasite Plasmodium. Although the disease-causing forms of the parasite exist only in the human blood, mosquitoes of the genus Anopheles are the obligate vector for transmission. Here, we review the parasite life cycle in the vector and highlight the human and mosquito contributions that limit malaria parasite development in the mosquito host. We address parasite killing in its mosquito host and bottlenecks in parasite numbers that might guide intervention strategies to prevent transmission. PMID:25185005

  3. Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

    Directory of Open Access Journals (Sweden)

    Dall’Olio Giovanni

    2012-06-01

    Full Text Available Abstract Background Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. Conclusions These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show

  4. Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

    Science.gov (United States)

    Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.

    2011-01-01

    Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

  5. Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes.

    Directory of Open Access Journals (Sweden)

    Hendrik Monsees

    Full Text Available In classical aquaponics (coupled aquaponic systems, 1-loop systems the production of fish in recirculating aquaculture systems (RAS and plants in hydroponics are combined in a single loop, entailing systemic compromises on the optimal production parameters (e.g. pH. Recently presented decoupled aquaponics (2-loop systems have been awarded for eliminating major bottlenecks. In a pilot study, production in an innovative decoupled aquaponic system was compared with a coupled system and, as a control, a conventional RAS, assessing growth parameters of fish (FCR, SGR and plants over an experimental period of 5 months. Soluble nutrients (NO3--N, NO2--N, NH4+-N, PO43-, K+, Ca2+, Mg2+, SO42-, Cl2- and Fe2+, elemental composition of plants, fish and sludge (N, P, K, Ca, Mg, Na, C, abiotic factors (temperature, pH, oxygen, and conductivity, fertilizer and water consumption were determined. Fruit yield was 36% higher in decoupled aquaponics and pH and fertilizer management was more effective, whereas fish production was comparable in both systems. The results of this pilot study clearly illustrate the main advantages of decoupled, two-loop aquaponics and demonstrate how bottlenecks commonly encountered in coupled aquaponics can be managed to promote application in aquaculture.

  6. A bottleneck model of set-specific capture.

    Directory of Open Access Journals (Sweden)

    Katherine Sledge Moore

    Full Text Available Set-specific contingent attentional capture is a particularly strong form of capture that occurs when multiple attentional sets guide visual search (e.g., "search for green letters" and "search for orange letters". In this type of capture, a potential target that matches one attentional set (e.g. a green stimulus impairs the ability to identify a temporally proximal target that matches another attentional set (e.g. an orange stimulus. In the present study, we investigated whether set-specific capture stems from a bottleneck in working memory or from a depletion of limited resources that are distributed across multiple attentional sets. In each trial, participants searched a rapid serial visual presentation (RSVP stream for up to three target letters (T1-T3 that could appear in any of three target colors (orange, green, or lavender. The most revealing findings came from trials in which T1 and T2 matched different attentional sets and were both identified. In these trials, T3 accuracy was lower when it did not match T1's set than when it did match, but only when participants failed to identify T2. These findings support a bottleneck model of set-specific capture in which a limited-capacity mechanism in working memory enhances only one attentional set at a time, rather than a resource model in which processing capacity is simultaneously distributed across multiple attentional sets.

  7. Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes.

    Science.gov (United States)

    Monsees, Hendrik; Kloas, Werner; Wuertz, Sven

    2017-01-01

    In classical aquaponics (coupled aquaponic systems, 1-loop systems) the production of fish in recirculating aquaculture systems (RAS) and plants in hydroponics are combined in a single loop, entailing systemic compromises on the optimal production parameters (e.g. pH). Recently presented decoupled aquaponics (2-loop systems) have been awarded for eliminating major bottlenecks. In a pilot study, production in an innovative decoupled aquaponic system was compared with a coupled system and, as a control, a conventional RAS, assessing growth parameters of fish (FCR, SGR) and plants over an experimental period of 5 months. Soluble nutrients (NO3--N, NO2--N, NH4+-N, PO43-, K+, Ca2+, Mg2+, SO42-, Cl2- and Fe2+), elemental composition of plants, fish and sludge (N, P, K, Ca, Mg, Na, C), abiotic factors (temperature, pH, oxygen, and conductivity), fertilizer and water consumption were determined. Fruit yield was 36% higher in decoupled aquaponics and pH and fertilizer management was more effective, whereas fish production was comparable in both systems. The results of this pilot study clearly illustrate the main advantages of decoupled, two-loop aquaponics and demonstrate how bottlenecks commonly encountered in coupled aquaponics can be managed to promote application in aquaculture.

  8. Helical bottleneck effect in 3D homogeneous isotropic turbulence

    Science.gov (United States)

    Stepanov, Rodion; Golbraikh, Ephim; Frick, Peter; Shestakov, Alexander

    2018-02-01

    We present the results of modelling the development of homogeneous and isotropic turbulence with a large-scale source of energy and a source of helicity distributed over scales. We use the shell model for numerical simulation of the turbulence at high Reynolds number. The results show that the helicity injection leads to a significant change in the behavior of the energy and helicity spectra in scales larger and smaller than the energy injection scale. We suggest the phenomenology for direct turbulent cascades with the helicity effect, which reduces the efficiency of the spectral energy transfer. Therefore the energy is accumulated and redistributed so that non-linear interactions will be sufficient to provide a constant energy flux. It can be interpreted as the ‘helical bottleneck effect’ which, depending on the parameters of the injection helicity, reminds one of the well-known bottleneck effect at the end of inertial range. Simulations which included the infrared part of the spectrum show that the inverse cascade hardly develops under distributed helicity forcing.

  9. Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel.

    Science.gov (United States)

    Bučková, Jana; Cerný, Viktor; Novelletto, Andrea

    2013-05-01

    The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past. Copyright © 2013 Wiley Periodicals, Inc.

  10. Patterns of population differentiation and natural selection on the celiac disease background risk network.

    Directory of Open Access Journals (Sweden)

    Aaron Sams

    Full Text Available Celiac disease is a common small intestinal inflammatory condition induced by wheat gluten and related proteins from rye and barley. Left untreated, the clinical presentation of CD can include failure to thrive, malnutrition, and distension in juveniles. The disease can additionally lead to vitamin deficiencies, anemia, and osteoporosis. Therefore, CD potentially negatively affected fitness in past populations utilizing wheat, barley, and rye. Previous analyses of CD risk variants have uncovered evidence for positive selection on some of these loci. These studies also suggest the possibility that risk for common autoimmune conditions such as CD may be the result of positive selection on immune related loci in the genome to fight infection. Under this evolutionary scenario, disease phenotypes may be a trade-off from positive selection on immunity. If this hypothesis is generally true, we can expect to find a signal of natural selection when we survey across the network of loci known to influence CD risk. This study examines the non-HLA autosomal network of gene loci associated with CD risk in Europe. We reject the null hypothesis of neutrality on this network of CD risk loci. Additionally, we can localize evidence of selection in time and space by adding information from the genome of the Tyrolean Iceman. While we can show significant differentiation between continental regions across the CD network, the pattern of evidence is not consistent with primarily recent (Holocene selection across this network in Europe. Further localization of ancient selection on this network may illuminate the ecological pressures acting on the immune system during this critically interesting phase of our evolution.

  11. Population differentiation in a Mediterranean relict shrub: the potential role of local adaptation for coping with climate change.

    Science.gov (United States)

    Lázaro-Nogal, Ana; Matesanz, Silvia; Hallik, Lea; Krasnova, Alisa; Traveset, Anna; Valladares, Fernando

    2016-04-01

    Plants can respond to climate change by either migrating, adapting to the new conditions or going extinct. Relict plant species of limited distribution can be especially vulnerable as they are usually composed of small and isolated populations, which may reduce their ability to cope with rapidly changing environmental conditions. The aim of this study was to assess the vulnerability of Cneorum tricoccon L. (Cneoraceae), a Mediterranean relict shrub of limited distribution, to a future drier climate. We evaluated population differentiation in functional traits related to drought tolerance across seven representative populations of the species' range. We measured morphological and physiological traits in both the field and the greenhouse under three water availability levels. Large phenotypic differences among populations were found under field conditions. All populations responded plastically to simulated drought, but they differed in mean trait values as well as in the slope of the phenotypic response. Particularly, dry-edge populations exhibited multiple functional traits that favored drought tolerance, such as more sclerophyllous leaves, strong stomatal control but high photosynthetic rates, which increases water use efficiency (iWUE), and an enhanced ability to accumulate sugars as osmolytes. Although drought decreased RGR in all populations, this reduction was smaller for populations from the dry edge. Our results suggest that dry-edge populations of this relict species are well adapted to drought, which could potentially mitigate the species' extinction risk under drier scenarios. Dry-edge populations not only have a great conservation value but can also change expectations from current species' distribution models.

  12. Habitat fragmentation influences gene structure and gene differentiation among the Loxoblemmus aomoriensis populations in the Thousand Island Lake.

    Science.gov (United States)

    Lv, Kun; Zhou, Jing; Gu, Jian-Qiang; Zhou, Guo-Xing; Wang, Wei; Xu, Zhi-Hong

    2017-02-16

    Thousand Island Lake (TIL) is a fragmented landscape consisting of more than 1000 land-bridge islands isolated during reservoir formation. To evaluate the effects of fragmentation and island attributes on insect populations, we examined the genetic structure of Loxoblemmus aomoriensis, a species of cricket widely distributed in TIL, and compared genetic diversity between islands samples. Population genetic analyses was conducted based on mitochondrial DNA haplotype frequencies of 10 sample islands. By comparing three island attributes with population genetic diversity reveals that island area influenced population genetic diversity (r(2 )=( )0.5094, p = 0.00204). Using Pairwise Fst values, we also found that long-distance isolation increased the genetic differentiation, while short-distance isolation can be offset by dispersal. These results indicate that fragmentation can impact populations on a genetic level.

  13. Transcriptome analysis deciphers evolutionary mechanisms underlying genetic differentiation between coastal and offshore anchovy populations in the Bay of Biscay

    KAUST Repository

    Montes, Iratxe

    2016-09-13

    Morphometry and otolith microchemistry point to the existence of two populations of the European anchovy (Engraulis encrasicolus) in the Bay of Biscay: one in open seawaters, and a yet unidentified population in coastal waters. To test this hypothesis, we assembled a large number of samples from the region, including 587 juveniles and spawning adults from offshore and coastal waters, and 264 fish from other locations covering most of the species’ European range. These samples were genotyped for 456 exonic SNPs that provide a robust way to decipher adaptive processes in these populations. Two genetically differentiated populations of anchovy inhabit the Bay of Biscay with different population dynamics: (1) a large offshore population associated with marine waters included in the wide-shelf group, and (2) a coastal metapopulation adapted to estuarine environments in the Bay of Biscay and North Sea included in the narrow-shelf group. Transcriptome analysis identified neutral and adaptive evolutionary processes underlying differentiation between these populations. Reduced gene flow between offshore and coastal populations in the Bay of Biscay appears to result from divergence between two previously isolated gene pools adapted to contrasting habitats and now in secondary contact. Eleven molecular markers appear to mark divergent selection between the ecotypes, and a majority of these markers are associated with salinity variability. Ecotype differences at two outlier genes, TSSK6 and basigin, may hinder gamete compatibility between the ecotypes and reinforce reproductive isolation. Additionally, possible convergent evolution between offshore and coastal populations in the Bay of Biscay has been detected for the syntaxin1B-otoferlin gene system, which is involved in the control of larval buoyancy. Further study of exonic markers opens the possibility of understanding the mechanisms of adaptive divergence between European anchovy populations. © 2016, Springer

  14. Microsatellites reveal substantial among-population genetic differentiation and strong inbreeding in the relict fern Dryopteris aemula.

    Science.gov (United States)

    Jiménez, Ares; Holderegger, Rolf; Csencsics, Daniela; Quintanilla, Luis G

    2010-07-01

    A previous study detected no allozyme diversity in Iberian populations of the buckler-fern Dryopteris aemula. The use of a more sensitive marker, such as microsatellites, was thus needed to reveal the genetic diversity, breeding system and spatial genetic structure of this species in natural populations. Eight microsatellite loci for D. aemula were developed and their cross-amplification with other ferns was tested. Five polymorphic loci were used to characterize the amount and distribution of genetic diversity of D. aemula in three populations from the Iberian Peninsula and one population from the Azores. Most microsatellite markers developed were transferable to taxa close to D. aemula. Overall genetic variation was low (H(T) = 0.447), but was higher in the Azorean population than in the Iberian populations of this species. Among-population genetic differentiation was high (F(ST) = 0.520). All loci strongly departed from Hardy-Weinberg equilibrium. In the population where genetic structure was studied, no spatial autocorrelation was found in any distance class. The higher genetic diversity observed in the Azorean population studied suggested a possible refugium in this region from which mainland Europe has been recolonized after the Pleistocene glaciations. High among-population genetic differentiation indicated restricted gene flow (i.e. lack of spore exchange) across the highly fragmented area occupied by D. aemula. The deviations from Hardy-Weinberg equilibrium reflected strong inbreeding in D. aemula, a trait rarely observed in homosporous ferns. The absence of spatial genetic structure indicated effective spore dispersal over short distances. Additionally, the cross-amplification of some D. aemula microsatellites makes them suitable for use in other Dryopteris taxa.

  15. Phenotypic and genetic differentiation among yellow monkeyflower populations from thermal and non-thermal soils in Yellowstone National Park.

    Science.gov (United States)

    Lekberg, Ylva; Roskilly, Beth; Hendrick, Margaret F; Zabinski, Catherine A; Barr, Camille M; Fishman, Lila

    2012-09-01

    In flowering plants, soil heterogeneity can generate divergent natural selection over fine spatial scales, and thus promote local adaptation in the absence of geographic barriers to gene flow. Here, we investigate phenotypic and genetic differentiation in one of the few flowering plants that thrives in both geothermal and non-thermal soils in Yellowstone National Park (YNP). Yellow monkeyflowers (Mimulus guttatus) growing at two geothermal ("thermal") sites in YNP were distinct in growth form and phenology from paired populations growing nearby ( 0.34), which were only weakly differentiated from each other (all F (ST) Yellowstone.

  16. Celebrity Suicides and Their Differential Influence on Suicides in the General Population: A National Population-Based Study in Korea

    Science.gov (United States)

    Myung, Woojae; Won, Hong-Hee; Fava, Maurizio; Mischoulon, David; Yeung, Albert; Lee, Dongsoo; Kim, Doh Kwan

    2015-01-01

    Objective Although evidence suggests that there is an increase in suicide rates in the general population following celebrity suicide, the rates are heterogeneous across celebrities and countries. It is unclear which is the more vulnerable population according to the effect sizes of celebrity suicides to general population. Methods All suicide victims in the general population verified by the Korea National Statistical Office and suicides of celebrity in South Korea were included for 7 years from 2005 to 2011. Effect sizes were estimated by comparing rates of suicide in the population one month before and after each celebrity suicide. The associations between suicide victims and celebrities were examined. Results Among 94,845 suicide victims, 17,209 completed suicide within one month after 13 celebrity suicides. Multivariate logistic regression analyses revealed that suicide victims who died after celebrity suicide were significantly likely to be of age 20-39, female, and to die by hanging. These qualities were more strongly associated among those who followed celebrity suicide with intermediate and high effect sizes than lower. Younger suicide victims were significantly associated with higher effect size, female gender, white collar employment, unmarried status, higher education, death by hanging, and night-time death. Characteristics of celebrities were significantly associated with those of general population in hanging method and gender. Conclusion Individuals who commit suicide after a celebrity suicide are likely to be younger, female, and prefer hanging as method of suicide, which are more strongly associated in higher effect sizes of celebrity suicide. PMID:25866521

  17. Celebrity suicides and their differential influence on suicides in the general population: a national population-based study in Korea.

    Science.gov (United States)

    Myung, Woojae; Won, Hong-Hee; Fava, Maurizio; Mischoulon, David; Yeung, Albert; Lee, Dongsoo; Kim, Doh Kwan; Jeon, Hong Jin

    2015-04-01

    Although evidence suggests that there is an increase in suicide rates in the general population following celebrity suicide, the rates are heterogeneous across celebrities and countries. It is unclear which is the more vulnerable population according to the effect sizes of celebrity suicides to general population. All suicide victims in the general population verified by the Korea National Statistical Office and suicides of celebrity in South Korea were included for 7 years from 2005 to 2011. Effect sizes were estimated by comparing rates of suicide in the population one month before and after each celebrity suicide. The associations between suicide victims and celebrities were examined. Among 94,845 suicide victims, 17,209 completed suicide within one month after 13 celebrity suicides. Multivariate logistic regression analyses revealed that suicide victims who died after celebrity suicide were significantly likely to be of age 20-39, female, and to die by hanging. These qualities were more strongly associated among those who followed celebrity suicide with intermediate and high effect sizes than lower. Younger suicide victims were significantly associated with higher effect size, female gender, white collar employment, unmarried status, higher education, death by hanging, and night-time death. Characteristics of celebrities were significantly associated with those of general population in hanging method and gender. Individuals who commit suicide after a celebrity suicide are likely to be younger, female, and prefer hanging as method of suicide, which are more strongly associated in higher effect sizes of celebrity suicide.

  18. Assessment of host-associated genetic differentiation among phenotypically divergent populations of a coral-eating gastropod across the Caribbean.

    Directory of Open Access Journals (Sweden)

    Lyza Johnston

    Full Text Available Host-associated adaptation is emerging as a potential driver of population differentiation and speciation for marine organisms with major implications for ecosystem structure and function. Coralliophila abbreviata are corallivorous gastropods that live and feed on most of the reef-building corals in the tropical western Atlantic and Caribbean. Populations of C. abbreviata associated with the threatened acroporid corals, Acropora palmata and A. cervicornis, display different behavioral, morphological, demographic, and life-history characteristics than those that inhabit other coral host taxa, indicating that host-specific selective forces may be acting on C. abbreviata. Here, we used newly developed polymorphic microsatellite loci and mitochondrial cytochrome b sequence data to assess the population genetic structure, connectivity, and demographic history of C. abbreviata populations from three coral host taxa (A. palmata, Montastraea spp., Mycetophyllia spp. and six geographic locations across the Caribbean. Analysis of molecular variance provided some evidence of weak and possibly geographically variable host-associated differentiation but no evidence of differentiation among sampling locations or major oceanographic regions, suggesting high gene flow across the Caribbean. Phylogenetic network and bayesian clustering analyses supported a hypothesis of a single panmictic population as individuals failed to cluster by host or sampling location. Demographic analyses consistently supported a scenario of population expansion during the Pleistocene, a time of major carbonate reef development in the region. Although further study is needed to fully elucidate the interactive effects of host-associated selection and high gene flow in this system, our results have implications for local and regional community interactions and impact of predation on declining coral populations.

  19. Low genetic diversity and high differentiation among relict populations of the neotropical gymnosperm Podocarpus sellowii (Klotz.) in the Atlantic Forest.

    Science.gov (United States)

    Dantas, Liliane G; Esposito, Tiago; de Sousa, Adna Cristina Barbosa; Félix, Leonardo; Amorim, Lidiane L B; Benko-Iseppon, Ana Maria; Batalha-Filho, Henrique; Pedrosa-Harand, Andrea

    2015-02-01

    Podocarpus sellowii (Podocarpaceae) is one of only a few gymnosperms native to Brazil and the sole species of the genus found in the northeastern region of that country. It has a very restricted distribution in this region, with only three known populations in highland forests (called Brejos de Altitude), which apparently have been isolated from each other since the Pleistocene. Due to this long-term isolation and the fact that these populations have few adult individuals and suffer great anthropogenic pressure, low genetic variability is expected, compromising their long-term viability. The present work assessed the genetic variability and structure of northeastern populations of P. sellowii to investigate the role of Pleistocene glaciations on the genetic relationships between them and to propose strategies for their conservation by analyzing the SSR and ISSR markers of adult and juvenile individuals. Low genetic diversity was found with both markers, associated with a high differentiation of the Brejo de Baturité population in relation to the others-suggesting their isolation at different points in time, probably during the Pleistocene. Actions directed towards increasing the genetic diversity of these populations will be needed, such as planting seedlings with high genetic variability-but the high degrees of differentiation observed between the populations must be taken into account.

  20. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases.

    Directory of Open Access Journals (Sweden)

    Roberto Amato

    Full Text Available Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or F(ST. We performed a genome-wide estimation of F(ST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of F(ST values between autosomes and heterochromosomes. When we compared the F(ST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of F(ST, while several pathways related to cell signalling, growth and morphogenesis showed high F(ST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.

  1. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations.

    Science.gov (United States)

    Angelone-Alasaad, Samer; Biebach, Iris; Pérez, Jesús M; Soriguer, Ramón C; Granados, José E

    2017-01-01

    Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies.

  2. Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: differentiation of subpopulations

    Directory of Open Access Journals (Sweden)

    Appukuttannair R. Pradeep

    2011-01-01

    Full Text Available Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei's genetic distance between populations increased significantly with altitude (R² = 0.71 and geographic distance (R² = 0.78. On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei's gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R² = 0.63. Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D'2IS exceeded D'2ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool.

  3. A hybrid shifting bottleneck-tabu search heuristic for the job shop total weighted tardiness problem

    OpenAIRE

    Bülbül, Kerem; Bulbul, Kerem

    2010-01-01

    In this paper, we study the job shop scheduling problem with the objective of minimizing the total weighted tardiness. We propose a hybrid shifting bottleneck - tabu search (SB-TS) algorithm by replacing the reoptimization step in the shifting bottleneck (SB) algorithm by a tabu search (TS). In terms of the shifting bottleneck heuristic, the proposed tabu search optimizes the total weighted tardiness for partial schedules in which some machines are currently assumed to have infinite capacity...

  4. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Directory of Open Access Journals (Sweden)

    Damien C Tully

    2016-05-01

    Full Text Available Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU, we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  5. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Science.gov (United States)

    Tully, Damien C; Ogilvie, Colin B; Batorsky, Rebecca E; Bean, David J; Power, Karen A; Ghebremichael, Musie; Bedard, Hunter E; Gladden, Adrianne D; Seese, Aaron M; Amero, Molly A; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B; Tinsley, Jake; Lennon, Niall J; Henn, Matthew R; Brumme, Zabrina L; Norris, Philip J; Rosenberg, Eric S; Mayer, Kenneth H; Jessen, Heiko; Kosakovsky Pond, Sergei L; Walker, Bruce D; Altfeld, Marcus; Carlson, Jonathan M; Allen, Todd M

    2016-05-01

    Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  6. Protein crystallization: Eluding the bottleneck of X-ray crystallography

    Science.gov (United States)

    Holcomb, Joshua; Spellmon, Nicholas; Zhang, Yingxue; Doughan, Maysaa; Li, Chunying; Yang, Zhe

    2017-01-01

    To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins. PMID:29051919

  7. Situation awareness of active distribution network: roadmap, technologies, and bottlenecks

    DEFF Research Database (Denmark)

    Lin, Jin; Wan, Can; Song, Yonghua

    2016-01-01

    With the rapid development of local generation and demand response, the active distribution network (ADN), which aggregates and manages miscellaneous distributed resources, has moved from theory to practice. Secure and optimal operations now require an advanced situation awareness (SA) system so...... in the project of developing an SA system as the basic component of a practical active distribution management system (ADMS) deployed in Beijing, China, is presented. This paper reviews the ADN’s development roadmap by illustrating the changes that are made in elements, topology, structure, and control scheme....... Taking into consideration these hardware changes, a systematic framework is proposed for the main components and the functional hierarchy of an SA system for the ADN. The SA system’s implementation bottlenecks are also presented, including, but not limited to issues in big data platform, distribution...

  8. Through the portal: Effect anticipation in the central bottleneck.

    Science.gov (United States)

    Wirth, Robert; Pfister, Roland; Janczyk, Markus; Kunde, Wilfried

    2015-09-01

    Ample evidence suggests that motor actions are generated by mentally recollecting their sensory consequences, i.e., via effect anticipations. There is less evidence, though, on the capacity limitations that such effect anticipations suffer from. In the present paper we aim to overcome shortcomings of previous research on this issue by extending the set of empirical indicators of effect anticipations and by using trial-wise instead of block-wise manipulations. In four experiments using the locus of slack- and the effect propagation-logic, we found conclusive evidence for effect anticipation taking place in the capacity-limited central bottleneck. These findings extend previous research suggesting an overlap of a "response selection" process as assumed in traditional stage theory and effect anticipation processes as assumed in effect-based ideomotor models of action control. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Queuing model of a traffic bottleneck with bimodal arrival rate

    Science.gov (United States)

    Woelki, Marko

    2016-06-01

    This paper revisits the problem of tuning the density in a traffic bottleneck by reduction of the arrival rate when the queue length exceeds a certain threshold, studied recently for variants of totally asymmetric simple exclusion process (TASEP) and Burgers equation. In the present approach, a simple finite queuing system is considered and its contrasting “phase diagram” is derived. One can observe one jammed region, one low-density region and one region where the queue length is equilibrated around the threshold. Despite the simplicity of the model the physics is in accordance with the previous approach: The density is tuned at the threshold if the exit rate lies in between the two arrival rates.

  10. On Bottleneck Product Rate Variation Problem with Batching

    Directory of Open Access Journals (Sweden)

    Shree Khadka

    2013-07-01

    Full Text Available The product rate variation problem minimizes the variation in the rate at which different models of a common base product are produced on the assembly lines with the assumption of negligible switch-over cost and unit processing time for each copy of each model. The assumption of significant setup and arbitrary processing times forces the problem to be a two phase problem. The first phase determines the size and the number of batches and the second one sequences the batches of models. In this paper, the bottleneck case i.e. the min-max case of the problem with a generalized objective function is formulated. A Pareto optimal solution is proposed and a relation between optimal sequences for the problem with different objective functions is investigated.

  11. Reducing Concurrency Bottlenecks in Parallel I/O Workloads

    Energy Technology Data Exchange (ETDEWEB)

    Manzanares, Adam C. [Los Alamos National Laboratory; Bent, John M. [Los Alamos National Laboratory; Wingate, Meghan [Los Alamos National Laboratory

    2011-01-01

    To enable high performance parallel checkpointing we introduced the Parallel Log Structured File System (PLFS). PLFS is middleware interposed on the file system stack to transform concurrent writing of one application file into many non-concurrently written component files. The promising effectiveness of PLFS makes it important to examine its performance for workloads other than checkpoint capture, notably the different ways that state snapshots may be later read, to make the case for using PLFS in the Exascale I/O stack. Reading a PLFS file involved reading each of its component files. In this paper we identify performance limitations on broader workloads in an early version of PLFS, specifically the need to build and distribute an index for the overall file, and the pressure on the underlying parallel file system's metadata server, and show how PLFS's decomposed components architecture can be exploited to alleviate bottlenecks in the underlying parallel file system.

  12. Genetic differentiation between introduced Central European sika and source populations in Japan: effects of isolation and demographic events

    Czech Academy of Sciences Publication Activity Database

    Krojerová-Prokešová, Jarmila; Barančeková, Miroslava; Kawata, Y.; Oshida, T.; Igota, H.; Koubek, Petr

    2017-01-01

    Roč. 19, č. 7 (2017), s. 2125-2141 ISSN 1387-3547 R&D Projects: GA ČR GA524/09/1569 Institutional support: RVO:68081766 Keywords : Bottleneck * Founder effect * Genetic diversity * Invasion * Microsatellite loci Subject RIV: EG - Zoology Impact factor: 2.473, year: 2016

  13. Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement.

    Directory of Open Access Journals (Sweden)

    Ji Yang

    Full Text Available Anthropogenic landscapes influence evolutionary processes such as population genetic differentiation, however, not every type of landscape features exert the same effect on a species, hence it is necessary to estimate their relative effect for species management and conservation. Przewalski's gazelle (Procapra przewalskii, which inhabits a human-altered area on Qinghai-Tibet Plateau, is one of the most endangered antelope species in the world. Here, we report a landscape genetic study on Przewalski's gazelle. We used skin and fecal samples of 169 wild gazelles collected from nine populations and thirteen microsatellite markers to assess the genetic effect of anthropogenic landscape features on this species. For comparison, the genetic effect of geographical distance and topography were also evaluated. We found significant genetic differentiation, six genetic groups and restricted dispersal pattern in Przewalski's gazelle. Topography, human settlement and road appear to be responsible for observed genetic differentiation as they were significantly correlated with both genetic distance measures [F(ST/(1-F(ST and F'(ST/(1-F'(ST] in Mantel tests. IBD (isolation by distance was also inferred as a significant factor in Mantel tests when genetic distance was measured as F(ST/(1-F(ST. However, using partial Mantel tests, AIC(c calculations, causal modeling and AMOVA analysis, we found that human settlement was the main factor shaping current genetic differentiation among those tested. Altogether, our results reveal the relative influence of geographical distance, topography and three anthropogenic landscape-type on population genetic differentiation of Przewalski's gazelle and provide useful information for conservation measures on this endangered species.

  14. Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range.

    Science.gov (United States)

    Clucas, Gemma V; Younger, Jane L; Kao, Damian; Rogers, Alex D; Handley, Jonathan; Miller, Gary D; Jouventin, Pierre; Nolan, Paul; Gharbi, Karim; Miller, Karen J; Hart, Tom

    2016-10-13

    Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion. We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes. The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds

  15. Differential response of olfactory sensory neuron populations to copper ion exposure in zebrafish.

    Science.gov (United States)

    Lazzari, Maurizio; Bettini, Simone; Milani, Liliana; Maurizii, Maria Gabriella; Franceschini, Valeria

    2017-02-01

    The peripheral olfactory system of fish is in direct contact with the external aqueous environment, so dissolved contaminants can easily impair sensory functions and cause neurobehavioral injuries. The olfactory epithelium of fish is arranged in lamellae forming a rosette in the olfactory cavity and contains three main types of olfactory sensory neurons (OSNs): ciliated (cOSNs) and microvillous olfactory sensory neurons (mOSNs), common to all vertebrates, and a third minor group of olfactory neurons, crypt cells, absent in tetrapods. Since copper is a ubiquitously diffusing olfactory toxicant and a spreading contaminant in urban runoff, we investigated the effect of low copper concentration on the three different OSNs in the olfactory epithelium of zebrafish, a model system widely used in biological research. Image analysis was applied for morphometry and quantification of immunohistochemically detected OSNs. Copper exposure resulted in an evident decrease in olfactory epithelium thickness. Moreover, after exposure, the lamellae of the dorsal and ventral halves of the olfactory rosettes showed a different increase in their sensory areas, suggesting a lateral migration of new cells into non-sensory regions. The results of the present study provide clear evidence of a differential response of the three neural cell populations of zebrafish olfactory mucosa after 96h of exposure to copper ions at the sublethal concentration of 30μgL(-1). Densitometric values of cONS, immunostained with anti-G αolf, decreased of about 60% compared to the control. When the fish were transferred to water without copper addition and examined after 3, 10 and 30days, we observed a partial restoration of anti-G αolf staining intensity to normal condition. The recovery of cOSNs appeared sustained by neuronal proliferation, quantified with anti-PCNA immunostaining, in particular in the early days after exposure. The densitometric analysis applied to mOSNs, immunostained with anti-TRPC2

  16. Differentiation between Carex arenaria L. populations at the eastern range margin based on female and male glumes variation

    OpenAIRE

    Lech Urbaniak; Izabella Maik; Daromiła Urbaniak

    2014-01-01

    480 spikes from 16 populations of Carex arenaria L. planted in an experimental garden were collected and analysed for 4 female and 4 male glumes each. The characteristic of the interpopulational differentiation on the area of Poland was based on multivariate analysis, Student t-test and the coefficients of variation. The separateness of three populations from the isolated inland stations - 3(Góra), 11 (Tuczno), 15 (Poznań) and individual character of - 2 (Wisełka), 6 (Sobieszewo) from the coa...

  17. The evolutionary consequences of habitat fragmentation: Body morphology and coloration differentiation among brook trout populations of varying size.

    Science.gov (United States)

    Zastavniouk, Carol; Weir, Laura K; Fraser, Dylan J

    2017-09-01

    A reduction in population size due to habitat fragmentation can alter the relative roles of different evolutionary mechanisms in phenotypic trait differentiation. While deterministic (selection) and stochastic (genetic drift) mechanisms are expected to affect trait evolution, genetic drift may be more important than selection in small populations. We examined relationships between mature adult traits and ecological (abiotic and biotic) variables among 14 populations of brook trout. These naturally fragmented populations have shared ancestry but currently exhibit considerable variability in habitat characteristics and population size (49 habitat variation or operational sex ratio than to population size, suggesting that selection may overcome genetic drift at small population size. Phenotype-environment associations were also stronger in females than males, suggesting that natural selection due to abiotic conditions may act more strongly on females than males. Our results suggest that natural and sexual-selective pressures on phenotypic traits change during the process of habitat fragmentation, and that these changes are largely contingent upon existing habitat conditions within isolated fragments. Our study provides an improved understanding of the ecological and evolutionary consequences of habitat fragmentation and lends insight into the ability of some small populations to respond to selection and environmental change.

  18. GENETIC DIFFERENTIATION BETWEEN NOBLE CRAYFISH, ASTACUS ASTACUS (L., POPULATIONS DETECTED BY MICROSATELLITE LENGTH VARIATION IN THE RDNA ITS1 REGION

    Directory of Open Access Journals (Sweden)

    EDSMAN L.

    2002-07-01

    Full Text Available The Internal Transcribed Spacer (ITS region of the nuclear ribosomal repeat was investigated in the search for a suitable genetic marker for population studies of the noble crayfish Astacus astacus (L.. DNA sequencing revealed the presence of two microsatellite insertions in ITS1. By designing highly specific PCR primers, adjacent to one of the insertions, we were able to use fragment analysis to explore the variation of the insertion in 642 specimens from 17 populations of crayfish from Sweden and former Yugoslavia. A new statistical test, the Population Divergence Test, was developed to assess statistical significance of divergence between populations. This test does not assume Mendelian inheritance. Our results demonstrate that different populations often produce characteristic fragment patterns, and that most, but not all, populations are genetically distinct, with high significance. The populations that cannot be significantly differentiated are situated in close geographic proximity to each other and belong to the same main river system, probably reflecting that these populations have had recent contact and that gene flow has occurred.

  19. FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3

    OpenAIRE

    Duan, Shiwei; Zhang, Wei; Cox, Nancy Jean; Dolan, Mary Eileen

    2008-01-01

    The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNPb129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differentiation through a ...

  20. NANOG restores the impaired myogenic differentiation potential of skeletal myoblasts after multiple population doublings

    Directory of Open Access Journals (Sweden)

    Aref Shahini

    2018-01-01

    Full Text Available Adult skeletal muscle regeneration relies on the activity of satellite cells residing in the skeletal muscle niche. However, systemic and intrinsic factors decrease the myogenic differentiation potential of satellite cells thereby impairing muscle regeneration. Here we present data showing that late passage C2C12 myoblasts exhibited significantly impaired myogenic differentiation potential that was accompanied by impaired expression of myogenic regulatory factors (Myf5, MyoD, Myogenin, and MRF4 and members of myocyte enhancer factor 2 family. Notably, ectopic expression of NANOG preserved the morphology and restored the myogenic differentiation capacity of late passage myoblasts, possibly by restoring the expression level of these myogenic factors. Muscle regeneration was effective in 2D cultures and in 3D skeletal microtissues mimicking the skeletal muscle niche. The presence of NANOG was required for at least 15 days to reverse the impaired differentiation potential of myoblasts. However, it was critical to remove NANOG during the process of maturation, as it inhibited myotube formation. Finally, myoblasts that were primed by NANOG maintained their differentiation capacity for 20 days after NANOG withdrawal, suggesting potential epigenetic changes. In conclusion, these results shed light on the potential of NANOG to restore the myogenic differentiation potential of myoblasts, which is impaired after multiple rounds of cellular division, and to reverse the loss of muscle regeneration.

  1. New evidence confirms that the mitochondrial bottleneck is generated without reduction of mitochondrial DNA content in early primordial germ cells of mice.

    Directory of Open Access Journals (Sweden)

    Liqin Cao

    2009-12-01

    Full Text Available In mammals, observations of rapid shifts in mitochondrial DNA (mtDNA variants between generations have led to the creation of the bottleneck theory for the transmission of mtDNA. The bottleneck could be attributed to a marked decline of mtDNA content in germ cells giving rise to the next generation, to a small effective number of mtDNA segregation units resulting from homoplasmic nucleoids rather than the single mtDNA molecule serving as the units of segregation, or to the selective transmission of a subgroup of the mtDNA population to the progeny. We have previously determined mtDNA copy number in single germ cells and shown that the bottleneck occurs without the reduction in germline mtDNA content. Recently one study suggested that the bottleneck is driven by a remarkable decline of mtDNA copies in early primordial germ cells (PGCs, while another study reported that the mtDNA genetic bottleneck results from replication of a subpopulation of the mtDNA genome during postnatal oocyte maturation and not during embryonic oogenesis, despite a detected a reduction in mtDNA content in early PGCs. To clarify these contradictory results, we examined the mtDNA copy number in PGCs isolated from transgenic mice expressing fluorescent proteins specifically in PGCs as in the aforementioned two other studies. We provide clear evidence to confirm that no remarkable reduction in mtDNA content occurs in PGCs and reinforce that the bottleneck is generated without reduction of mtDNA content in germ cells.

  2. New evidence confirms that the mitochondrial bottleneck is generated without reduction of mitochondrial DNA content in early primordial germ cells of mice.

    Science.gov (United States)

    Cao, Liqin; Shitara, Hiroshi; Sugimoto, Michihiko; Hayashi, Jun-Ichi; Abe, Kuniya; Yonekawa, Hiromichi

    2009-12-01

    In mammals, observations of rapid shifts in mitochondrial DNA (mtDNA) variants between generations have led to the creation of the bottleneck theory for the transmission of mtDNA. The bottleneck could be attributed to a marked decline of mtDNA content in germ cells giving rise to the next generation, to a small effective number of mtDNA segregation units resulting from homoplasmic nucleoids rather than the single mtDNA molecule serving as the units of segregation, or to the selective transmission of a subgroup of the mtDNA population to the progeny. We have previously determined mtDNA copy number in single germ cells and shown that the bottleneck occurs without the reduction in germline mtDNA content. Recently one study suggested that the bottleneck is driven by a remarkable decline of mtDNA copies in early primordial germ cells (PGCs), while another study reported that the mtDNA genetic bottleneck results from replication of a subpopulation of the mtDNA genome during postnatal oocyte maturation and not during embryonic oogenesis, despite a detected a reduction in mtDNA content in early PGCs. To clarify these contradictory results, we examined the mtDNA copy number in PGCs isolated from transgenic mice expressing fluorescent proteins specifically in PGCs as in the aforementioned two other studies. We provide clear evidence to confirm that no remarkable reduction in mtDNA content occurs in PGCs and reinforce that the bottleneck is generated without reduction of mtDNA content in germ cells.

  3. Population stochastic modelling (PSM)--an R package for mixed-effects models based on stochastic differential equations.

    Science.gov (United States)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode; Overgaard, Rune Viig; Madsen, Henrik

    2009-06-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model development, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 109-141; C.W. Tornøe, R.V. Overgaard, H. Agersø, H.A. Nielsen, H. Madsen, E.N. Jonsson, Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations, Pharm. Res. 22 (August(8)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornøe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODEs) with an observation link that incorporates noise. This state-space formulation only allows for observation noise and not for system noise. Extending to SDEs allows for a Wiener noise component in the system equations. This additional noise component enables handling of autocorrelated residuals originating from natural variation or systematic model error. Autocorrelated residuals are often partly ignored in PK/PD modelling although violating the hypothesis for many standard statistical tests. This article presents a package for the statistical program R that is able to handle SDEs in a mixed-effects setting. The estimation method implemented is the FOCE(1) approximation to the population likelihood which is generated from the individual likelihoods that are approximated using the Extended Kalman Filter's one-step predictions.

  4. Genetic variability and differentiation among populations of the Azorean endemic gymnosperm Juniperus brevifolia: baseline information for a conservation and restoration perspective.

    Science.gov (United States)

    Silva, Luís; Elias, Rui B; Moura, Mónica; Meimberg, Harald; Dias, Eduardo

    2011-12-01

    The Azorean endemic gymnosperm Juniperus brevifolia (Seub.) Antoine is a top priority species for conservation in Macaronesia, based on its ecological significance in natural plant communities. To evaluate genetic variability and differentiation among J. brevifolia populations from the Azorean archipelago, we studied 15 ISSR and 15 RAPD markers in 178 individuals from 18 populations. The average number of polymorphic bands per population was 65 for both ISSR and RAPD. The majority of genetic variability was found within populations and among populations within islands, and this partitioning of variability was confirmed by AMOVA. The large majority of population pairwise F(ST) values were above 0.3 and below 0.6. The degree of population genetic differentiation in J. brevifolia was relatively high compared with other species, including Juniperus spp. The genetic differentiation among populations suggests that provenance should be considered when formulating augmentation or reintroduction strategies.

  5. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    Science.gov (United States)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  6. Genetic diversity and population differentiation of chestnut blight fungus, Cryphonectria parasitica, in China as revealed by RAPD.

    Science.gov (United States)

    Yan, Boqian; Li, Zuozhou; Huang, Hongwen; Qin, Ling

    2007-06-01

    Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon's index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G (ST) = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N (m) (G (SR)) = 2.8 and N (m) (G (RT)) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.

  7. Morphological differentiation of seven parthenogenetic Artemia (Crustacea: Branchiopoda) populations from China, with special emphasis on ploidy degrees.

    Science.gov (United States)

    Asem, Alireza; Sun, Shi-Chun

    2016-04-01

    Parthenogenetic Artemia from seven Chinese locations with different elevations and various ploidies are characterized by phenotypic and morphometric analyses. Our findings show that the studied populations exhibit dissimilar patterns of ovisac. Four phenotypic patterns of furca are qualified and one of them is shared among di-, tetra- and pentaploid Artemia. Results of discriminant analysis based on morphometric data reveal that tetra- and pentaploid populations are grouped together, but the Aqqikkol Lake population is clearly differentiated. Previous hypothesis/conclusion that polyploid Artemia are larger than diploids is only partly supported by the present results, which show that pentaploid and tetraploid populations are larger than the mostly diploid populations in terms of the total length, but the body size of the Aibi Lake triploids has not significant difference with the sympatric diploids and the mostly diploid Aqqikkol population that inhabit in very high altitude has the largest body size among all parthenogenetic populations. The founding confirms that body size of Artemia is following with Bergmann's rule. © 2016 Wiley Periodicals, Inc.

  8. Assessing the genetic influence of ancient sociopolitical structure: micro-differentiation patterns in the population of Asturias (Northern Spain).

    Science.gov (United States)

    Pardiñas, Antonio F; Roca, Agustín; García-Vazquez, Eva; López, Belén

    2012-01-01

    The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as "micro-differentiation". It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.

  9. Assessing the genetic influence of ancient sociopolitical structure: micro-differentiation patterns in the population of Asturias (Northern Spain.

    Directory of Open Access Journals (Sweden)

    Antonio F Pardiñas

    Full Text Available The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as "micro-differentiation". It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.

  10. Differential response of olfactory sensory neuron populations to copper ion exposure in zebrafish

    Energy Technology Data Exchange (ETDEWEB)

    Lazzari, Maurizio, E-mail: maurizio.lazzari@unibo.it; Bettini, Simone; Milani, Liliana; Maurizii, Maria Gabriella; Franceschini, Valeria

    2017-02-15

    Highlights: • Copper exposure affects ciliated olfactory receptors more than microvillar cells. • Crypt olfactory sensory neurons are not affected by copper exposure. • Copper exposure induces an increase in the amount of sensory epithelium. - Abstract: The peripheral olfactory system of fish is in direct contact with the external aqueous environment, so dissolved contaminants can easily impair sensory functions and cause neurobehavioral injuries. The olfactory epithelium of fish is arranged in lamellae forming a rosette in the olfactory cavity and contains three main types of olfactory sensory neurons (OSNs): ciliated (cOSNs) and microvillous olfactory sensory neurons (mOSNs), common to all vertebrates, and a third minor group of olfactory neurons, crypt cells, absent in tetrapods. Since copper is a ubiquitously diffusing olfactory toxicant and a spreading contaminant in urban runoff, we investigated the effect of low copper concentration on the three different OSNs in the olfactory epithelium of zebrafish, a model system widely used in biological research. Image analysis was applied for morphometry and quantification of immunohistochemically detected OSNs. Copper exposure resulted in an evident decrease in olfactory epithelium thickness. Moreover, after exposure, the lamellae of the dorsal and ventral halves of the olfactory rosettes showed a different increase in their sensory areas, suggesting a lateral migration of new cells into non-sensory regions. The results of the present study provide clear evidence of a differential response of the three neural cell populations of zebrafish olfactory mucosa after 96 h of exposure to copper ions at the sublethal concentration of 30 μg L{sup −1}. Densitometric values of cONS, immunostained with anti-G {sub αolf}, decreased of about 60% compared to the control. When the fish were transferred to water without copper addition and examined after 3, 10 and 30 days, we observed a partial restoration of anti-G {sub

  11. Rapid evolution leads to differential population dynamics and top-down control in resurrectedDaphniapopulations.

    Science.gov (United States)

    Goitom, Eyerusalem; Kilsdonk, Laurens J; Brans, Kristien; Jansen, Mieke; Lemmens, Pieter; De Meester, Luc

    2018-01-01

    There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco-evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow-up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top-down control of phytoplankton. We inoculated populations of the water flea D. magna derived from three time periods of the same natural population known to have genetically adapted to changes in predation pressure in replicate mesocosms and monitored both Daphnia population densities and phytoplankton biomass in the presence and absence of fish. Our results revealed differences in population dynamics and top-down control of algae between mesocosms harboring populations from the time period before, during, and after a peak in fish predation pressure caused by human fish stocking. The differences, however, deviated from our a priori expectations. An S-map approach on time series revealed that the interactions between adults and juveniles strongly impacted the dynamics of populations and their top-down control on algae in the mesocosms, and that the strength of these interactions was modulated by rapid evolution as it occurred in nature. Our study provides an example of an evolutionary response that fundamentally alters the processes structuring population dynamics and impacts ecosystem features.

  12. Genetic differentiation across the Western Pacific populations of the hydrothermal vent bivalve Bathymodiolus spp. and the Eastern Pacific (13°N) population of Bathymodiolus thermophilus

    Science.gov (United States)

    Moraga, Dario; Jollivet, Didier; Denis, Françoise

    1994-10-01

    Deep-sea mussels, closely related to the Bathymodiolus genus and individuals of Bathymodiolus thermophilus, were collected on hydrothermal vents of the Lau and North-Fiji back-arc basins (Western Pacific) and at 13°N on the East Pacific Rise, respectively. Separate tissue homogenates were submitted to starch gel electrophoresis in order to study the genetic structure of the populations at 11 enzyme loci. Significant departures from the Hardy-Weinberg equilibrium were found at Aat-1, Gpi and Pgm loci without any location specificity. All the observed departures corresponded to heterozygote deficiencies that are common in mollusc bivalves. The genetic variability of these mussels was low in all samples, especially for the North-Fiji population. The genetic distances measured between populations demonstrated that significant genetic differentiation occurs between the Western Pacific mussel populations and the Eastern Pacific B. thermophilus, whereas gene flow appeared to be maintained between the two back-arc basins. The presence of both shared heterozygotes and genetic distances found between the western and the eastern populations do not allow us to separate these allopatric forms as distinct sibling species.

  13. Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791: a bivalve with planktonic larval dispersion

    Directory of Open Access Journals (Sweden)

    Cinthya Cristina Bulhões Arruda

    2009-01-01

    Full Text Available Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe and both H5 and H9 (Prainha and Acupe. Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted.

  14. Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791): A bivalve with planktonic larval dispersion

    Science.gov (United States)

    2009-01-01

    Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe) and both H5 and H9 (Prainha and Acupe). Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted. PMID:21637701

  15. Distribution of the cladoceran Bosmina huaronensis Delachaux, 1918 and niche differentiation among populations from different biogeographic regions

    Directory of Open Access Journals (Sweden)

    Lourdes M. A. Elmoor-Loureiro

    Full Text Available Described from a high-altitude lake in Peru, Bosmina huaronensis Delachaux, 1918 has been recorded in diverse kinds of water bodies in South and North America, suggesting that this species has high environmental tolerance and a wide niche breadth. The present study surveyed the occurrence records of B. huaronensis from 55 localities and, using multivariate analysis, investigated the niche differentiation among populations from different biogeographic regions, based on altitude and seven climatic variables. The first two principal components (PC explained 73% of the overall variance. PC1 was related to annual mean temperature, precipitation of driest quarter, and annual precipitation. PC2 was related to temperature seasonality and precipitation of wettest quarter. The PCA diagram showed three population groups, occupying different climate niches: (1 tropical highlands; (2 Neotropical lowlands; (3 temperate zones of both hemispheres. These results point to the need for further evaluation of these populations under morphological, genetic and ecological aspects.

  16. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

    Science.gov (United States)

    Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva-Cañas, José L; Vlasova, Anna; Marcet-Houben, Marina; Martínez-Cruz, Begoña; Cheng, Jade Yu; Prieto, Pablo; Quesada, Víctor; Quilez, Javier; Li, Gang; García, Francisca; Rubio-Camarillo, Miriam; Frias, Leonor; Ribeca, Paolo; Capella-Gutiérrez, Salvador; Rodríguez, José M; Câmara, Francisco; Lowy, Ernesto; Cozzuto, Luca; Erb, Ionas; Tress, Michael L; Rodriguez-Ales, Jose L; Ruiz-Orera, Jorge; Reverter, Ferran; Casas-Marce, Mireia; Soriano, Laura; Arango, Javier R; Derdak, Sophia; Galán, Beatriz; Blanc, Julie; Gut, Marta; Lorente-Galdos, Belen; Andrés-Nieto, Marta; López-Otín, Carlos; Valencia, Alfonso; Gut, Ivo; García, José L; Guigó, Roderic; Murphy, William J; Ruiz-Herrera, Aurora; Marques-Bonet, Tomas; Roma, Guglielmo; Notredame, Cedric; Mailund, Thomas; Albà, M Mar; Gabaldón, Toni; Alioto, Tyler; Godoy, José A

    2016-12-14

    Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.

  17. Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event

    Science.gov (United States)

    2010-01-01

    Background Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Results Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary

  18. Aging and differentiation in yeast populations: elders with different properties and functions

    Czech Academy of Sciences Publication Activity Database

    Palková, Z.; Wilkinson, D.; Váchová, Libuše

    2014-01-01

    Roč. 14, č. 1 (2014), s. 96-108 ISSN 1567-1356 R&D Projects: GA ČR GA13-08605S Institutional support: RVO:61388971 Keywords : yeast colonies * stationary-phase liquid cultures * comparison of differentiated cell subpopulations Subject RIV: EE - Microbiology, Virology Impact factor: 2.818, year: 2014

  19. The Effect of Differential Item Functioning in Anchor Items on Population Invariance of Equating

    Science.gov (United States)

    Huggins, Anne Corinne

    2014-01-01

    Invariant relationships in the internal mechanisms of estimating achievement scores on educational tests serve as the basis for concluding that a particular test is fair with respect to statistical bias concerns. Equating invariance and differential item functioning are both concerned with invariant relationships yet are treated separately in the…

  20. Genetic consequences of population decline in the European otter ( Lutra lutra ) : an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993

    DEFF Research Database (Denmark)

    Pertoldi, C.; Hansen, Michael Møller; Loeschcke, V.

    2001-01-01

    into the dynamics of the population decline. This was done by analysing microsatellite DNA variation in contemporary and historical samples, the latter encompassing DNA samples extracted from museum specimens covering a time-span from the 1880s to the 1960s. Tests for differences in expected heterozygosity...... and the numbers of alleles in contemporary versus historical samples and a test for detecting population bottlenecks provided few indications of a recent bottleneck and loss of variability. However, a procedure for detecting population expansions and declines, based on the genealogical history of microsatellite...... alleles, suggested that a drastic long-term population decline has taken place, which could have started more than 2000 years ago, possibly due to ancient anthropogenic pressure. Finally, assignment tests and pairwise F-ST values suggested weak but statistically significant genetic differentiation between...

  1. Genetic diversity and geographic differentiation in the alternative legume Tripodion tetraphyllum (L.) Fourr. in North African populations.

    Science.gov (United States)

    Bellucci, E; Nanni, L; Bitocchi, E; Rossi, M; Papa, R

    2011-03-01

    Wild legumes constitute an important component of widespread pastures in the Mediterranean basin. This region is experiencing remarkable effects from climate change, and continuous monitoring of species and population dynamics is important in order to plan and enact valuable conservation programmes. Tripodion tetraphyllum (L.) Fourr. [=Anthyllis tetraphylla L.] (2n=16), belongs to the tribe Loteae (Fabaceae), and could be very important for soil protection and sward improvement in abandoned or degraded Mediterranean areas. This alternative pasture legume is very closely related to Lotus japonicus and has some important characteristics for survival of the species in difficult and overgrazed Mediterranean areas. In this study, we have investigated the molecular diversity and population structure of T. tetraphyllum from North Africa using ISSR markers and plastidial microsatellites. To date, this is the first study concerning the genetic diversity and geographic differentiation of T. tetraphyllum. Ninety genotypes from three North African countries were analysed according to ISSRs, cpSSRs and one phenotypic trait. T. tetraphyllum shows a clear geographical structure, with differentiation associated with longitudinal differences; moreover, there is a general reduction in genetic diversity from Morocco to Tunisia. With all the markers used, strong differentiation was seen among collection sites. Our data highlight a genetic diversity gradient and cline of distribution, indicating that T. tetraphyllum has extended its area of distribution from Morocco to Tunisia. © 2010 German Botanical Society and The Royal Botanical Society of the Netherlands.

  2. Inter-population ovarian fluid variation differentially modulates sperm motility in Atlantic cod Gadus morhua.

    Science.gov (United States)

    Beirão, J; Purchase, C F; Wringe, B F; Fleming, I A

    2015-07-01

    This study tested the hypothesis that the effects of Atlantic cod Gadus morhua ovarian fluid on sperm motility variables are population specific. Sperm from a northern G. morhua population were activated in the presence of ovarian fluid from either northern or southern G. morhua at different concentrations. Ovarian fluid acted as a filter, in some cases reducing sperm swimming performance compared with seawater. Fluid from females foreign in population (southern) to the males (northern) had a greater inhibiting effect than those from the native population. Follow-up analysis indicated that the ovarian fluids had lower Ca(2+) concentration in northern than southern G. morhua, which could be the causative mechanism. If widespread, such cryptic female choice could reduce the incidence of intraspecific hybridization among diverged populations and contribute to reproductive isolation. © 2015 The Fisheries Society of the British Isles.

  3. Population differentiation and behavioural association of the two 'personality' genes DRD4 and SERT in dunnocks (Prunella modularis).

    Science.gov (United States)

    Holtmann, B; Grosser, S; Lagisz, M; Johnson, S L; Santos, E S A; Lara, C E; Robertson, B C; Nakagawa, S

    2016-02-01

    Quantifying the variation in behaviour-related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non-native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two 'personality' genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced (New Zealand, NZ) population of dunnocks, Prunella modularis. The NZ population showed a significantly lower number of single nucleotide polymorphisms (SNPs) compared to the UK population. Standardized F'st estimates of the personality genes and neutral microsatellites indicate that selection (anthropogenic and natural) probably occurred during and post the introduction event. Notably, the largest genetic differentiation was found in the intronic regions of the genes. In the NZ population, we also examined the association between polymorphisms in DRD4 and SERT and two highly repeatable behavioural traits: flight-initiation distance and mating status (promiscuous females and cobreeding males). We found 38 significant associations (for different allele effect models) between the two behavioural traits and the studied genes. Further, 22 of the tested associations showed antagonistic allele effects for males and females. Our findings illustrate how introduction events and accompanying ecological changes could influence the genetic diversity of behaviour-related genes. © 2015 John Wiley & Sons Ltd.

  4. Population differentiation for germination and early seedling root growth traits under saline conditions in the annual legume Medicago truncatula (Fabaceae).

    Science.gov (United States)

    Cordeiro, Matilde A; Moriuchi, Ken S; Fotinos, Tonya D; Miller, Kelsey E; Nuzhdin, Sergey V; von Wettberg, Eric J; Cook, Douglas R

    2014-03-01

    Seedling establishment and survival are highly sensitive to soil salinity and plants that evolved in saline environments are likely to express traits that increase fitness in those environments. Such traits are of ecological interest and they may have practical value for improving salt tolerance in cultivated species. We examined responses to soil salinity and tested potential mechanisms of salt tolerance in Medicago truncatula, using genotypes that originated from natural populations occurring on saline and nonsaline soils. Germination and seedling responses were quantified and compared between saline and nonsaline origin genotypes. Germination treatments included a range of sodium chloride (NaCl) concentrations in both offspring and parental environments. Seedling treatments included NaCl, abscisic acid (ABA), and potassium chloride (KCl). Saline origin genotypes displayed greater salinity tolerance for germination and seedling traits relative to nonsaline origin genotypes. We observed population specific differences for the effects of salinity on time to germination and for the impact of parental environment on germination rates. ABA and NaCl treatments had similar negative effects on root growth, although relative sensitivities differed, with saline population less sensitive to NaCl and more sensitive to ABA compared to their nonsaline counterparts. We report population differentiation for germination and seedling growth traits under saline conditions among populations derived from saline and nonsaline environments. These observations are consistent with a syndrome of adaptations for salinity tolerance during early plant development, including traits that are common among saline environments and those that are idiosyncratic to local populations.

  5. Marked Genetic Differentiation between Western Iberian and Italic Populations of the Olive Fly: Southern France as an Intermediate Area.

    Directory of Open Access Journals (Sweden)

    Barbara van Asch

    Full Text Available The olive fly, Bactrocera oleae, is the most important pest affecting the olive industry, to which it is estimated to cause average annual losses in excess of one billion dollars. As with other insects with a wide distribution, it is generally accepted that the understanding of B. oleae population structure and dynamics is fundamental for the design and implementation of effective monitoring and control strategies. However, and despite important advances in the past decade, a clear picture of B. oleae's population structure is still lacking. In the Mediterranean basin, where more than 95% of olive production is concentrated, evidence from several studies suggests the existence of three distinct sub-populations, but the geographical limits of their distributions, and the level of interpenetration and gene flow among them remain ill-characterized. Here we use mitochondrial haplotype analysis to show that one of the Mediterranean mitochondrial lineages displays geographically correlated substructure and demonstrate that Italic populations, though markedly distinct from their Iberian and Levantine counterparts are more diverse than previously described. Finally, we show that this distinction does not result from extant hypothetical geographic limits imposed by the Alps or the Pyrenees nor, more generally, does it result from any sharp boundary, as intermixing is observed in a broad area, albeit at variable levels. Instead, Bayesian phylogeographic analysis suggests the interplay between isolation-mediated differentiation during glacial periods and bi-directional dispersal and population intermixing in the interglacials has played a major role in shaping current olive fly population structure.

  6. Genetic differentiation in red-bellied piranha populations (Pygocentrus nattereri, Kner, 1858) from the Solimões-Amazonas River.

    Science.gov (United States)

    Dos Santos, Carlos Henrique Dos A; de Sá Leitão, Carolina S; Paula-Silva, Maria de N; Almeida-Val, Vera Maria F

    2016-06-01

    Red-bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões-Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red-bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red-bellied piranha populations collected at different locations of Solimões-Amazonas River system. We collected 234 red-bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões-Amazonas River system, with significant genetic differentiation between them. The red-bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing.

  7. Bottlenecks of motion processing during a visual glance: the leaky flask model.

    Directory of Open Access Journals (Sweden)

    Haluk Öğmen

    Full Text Available Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic memory, visual short-term memory (VSTM, and long-term memory (LTM. It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

  8. Analysis of registered CDM projects: potential removal of evidenced bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    Agosto, D.; Bombard, P.; Gostinelli, F.

    2007-07-01

    The Clean Development Mechanism (CDM) has developed during its first period of implementation, a distinctive set of patterns. The authors thought of concentrating on the CDM analysis in order to highlight potential remedies or reasons for given bottlenecks. In order to establish a sort of extensive SWOT analysis for CDMs, all the 356 projects actually (November 2006) registered at UNFCCC were examined, together with all the about 1000 PDDs presented to the UNFCCC but not registered yet. The CDM projects have been studied trying to cluster projects according to relevant characteristics, both from a technical and an economic point of view. Chosen indicators are meant to identify: more convenient/more diffused energy system for a CDM; reasons for a geographical distribution of different types of projects; potentials for a future exploitation of lower used technologies in CDM. Conclusions are drawn and appropriate tables and graphs presented. (1) the Baseline Emission Factor, combined to economic patterns, is the pivotal factor that characterizes both choices of host country and technology; (2) some technologies can exploit appropriately CDM scheme, whilst other technologies, are constrained by it. (3) there are still some important weak points: grouping of non Annex I countries; crediting period; criteria for the evaluation of sustainable development. (auth)

  9. Parsing a cognitive task: a characterization of the mind's bottleneck.

    Directory of Open Access Journals (Sweden)

    Mariano Sigman

    2005-02-01

    Full Text Available Parsing a mental operation into components, characterizing the parallel or serial nature of this flow, and understanding what each process ultimately contributes to response time are fundamental questions in cognitive neuroscience. Here we show how a simple theoretical model leads to an extended set of predictions concerning the distribution of response time and its alteration by simultaneous performance of another task. The model provides a synthesis of psychological refractory period and random-walk models of response time. It merely assumes that a task consists of three consecutive stages-perception, decision based on noisy integration of evidence, and response-and that the perceptual and motor stages can operate simultaneously with stages of another task, while the central decision process constitutes a bottleneck. We designed a number-comparison task that provided a thorough test of the model by allowing independent variations in number notation, numerical distance, response complexity, and temporal asynchrony relative to an interfering probe task of tone discrimination. The results revealed a parsing of the comparison task in which each variable affects only one stage. Numerical distance affects the integration process, which is the only step that cannot proceed in parallel and has a major contribution to response time variability. The other stages, mapping the numeral to an internal quantity and executing the motor response, can be carried out in parallel with another task. Changing the duration of these processes has no significant effect on the variance.

  10. Nepal health sector decentralization in limbo: what are the bottlenecks?

    Science.gov (United States)

    Gurung, G

    2011-06-01

    Nepal's efforts to decentralize its governance date back to over half a century. These efforts remained incomplete due to different reasons including administrative responses and political development affecting its implementation. The Local Self Governance Act (LSGA), 1999 envisaged, for the first time, to decentralize governance in the health sector through devolution of responsibilities, authority and resources to the local bodies. However, the pace of health sector decentralization in Nepal even after the LSGA was enacted has not progressed satisfactorily due to different reasons. The purpose of this paper is to discuss why health sector decentralization in Nepal has not advanced as expected. This paper identifies many issues--policy related, political, functional, and institutional--as stumbling blocks for health sector decentralization of Nepal. More specifically, the major bottlenecks for progress are lack of a clear cut policy, poor coordination among different sectors, improper handover process, lack of elected bodies, poor selection process of management committees, lack of coherence in the capacity building process of local bodies, ongoing debate about state restructuring including federalism and different political ideologies on decentralization.

  11. Bottleneck in secretion of α-amylase in Bacillus subtilis.

    Science.gov (United States)

    Yan, Shaomin; Wu, Guang

    2017-07-19

    Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.

  12. Eye shape and the nocturnal bottleneck of mammals.

    Science.gov (United States)

    Hall, Margaret I; Kamilar, Jason M; Kirk, E Christopher

    2012-12-22

    Most vertebrate groups exhibit eye shapes that vary predictably with activity pattern. Nocturnal vertebrates typically have large corneas relative to eye size as an adaptation for increased visual sensitivity. Conversely, diurnal vertebrates generally demonstrate smaller corneas relative to eye size as an adaptation for increased visual acuity. By contrast, several studies have concluded that many mammals exhibit typical nocturnal eye shapes, regardless of activity pattern. However, a recent study has argued that new statistical methods allow eye shape to accurately predict activity patterns of mammals, including cathemeral species (animals that are equally likely to be awake and active at any time of day or night). Here, we conduct a detailed analysis of eye shape and activity pattern in mammals, using a broad comparative sample of 266 species. We find that the eye shapes of cathemeral mammals completely overlap with nocturnal and diurnal species. Additionally, most diurnal and cathemeral mammals have eye shapes that are most similar to those of nocturnal birds and lizards. The only mammalian clade that diverges from this pattern is anthropoids, which have convergently evolved eye shapes similar to those of diurnal birds and lizards. Our results provide additional evidence for a nocturnal 'bottleneck' in the early evolution of crown mammals.

  13. HIV/AIDS: global trends, global funds and delivery bottlenecks

    Science.gov (United States)

    Coovadia, Hoosen M; Hadingham, Jacqui

    2005-01-01

    Globalisation affects all facets of human life, including health and well being. The HIV/AIDS epidemic has highlighted the global nature of human health and welfare and globalisation has given rise to a trend toward finding common solutions to global health challenges. Numerous international funds have been set up in recent times to address global health challenges such as HIV. However, despite increasingly large amounts of funding for health initiatives being made available to poorer regions of the world, HIV infection rates and prevalence continue to increase world wide. As a result, the AIDS epidemic is expanding and intensifying globally. Worst affected are undoubtedly the poorer regions of the world as combinations of poverty, disease, famine, political and economic instability and weak health infrastructure exacerbate the severe and far-reaching impacts of the epidemic. One of the major reasons for the apparent ineffectiveness of global interventions is historical weaknesses in the health systems of underdeveloped countries, which contribute to bottlenecks in the distribution and utilisation of funds. Strengthening these health systems, although a vital component in addressing the global epidemic, must however be accompanied by mitigation of other determinants as well. These are intrinsically complex and include social and environmental factors, sexual behaviour, issues of human rights and biological factors, all of which contribute to HIV transmission, progression and mortality. An equally important factor is ensuring an equitable balance between prevention and treatment programmes in order to holistically address the challenges presented by the epidemic. PMID:16060961

  14. HIV/AIDS: global trends, global funds and delivery bottlenecks

    Directory of Open Access Journals (Sweden)

    Hadingham Jacqui

    2005-08-01

    Full Text Available Abstract Globalisation affects all facets of human life, including health and well being. The HIV/AIDS epidemic has highlighted the global nature of human health and welfare and globalisation has given rise to a trend toward finding common solutions to global health challenges. Numerous international funds have been set up in recent times to address global health challenges such as HIV. However, despite increasingly large amounts of funding for health initiatives being made available to poorer regions of the world, HIV infection rates and prevalence continue to increase world wide. As a result, the AIDS epidemic is expanding and intensifying globally. Worst affected are undoubtedly the poorer regions of the world as combinations of poverty, disease, famine, political and economic instability and weak health infrastructure exacerbate the severe and far-reaching impacts of the epidemic. One of the major reasons for the apparent ineffectiveness of global interventions is historical weaknesses in the health systems of underdeveloped countries, which contribute to bottlenecks in the distribution and utilisation of funds. Strengthening these health systems, although a vital component in addressing the global epidemic, must however be accompanied by mitigation of other determinants as well. These are intrinsically complex and include social and environmental factors, sexual behaviour, issues of human rights and biological factors, all of which contribute to HIV transmission, progression and mortality. An equally important factor is ensuring an equitable balance between prevention and treatment programmes in order to holistically address the challenges presented by the epidemic.

  15. Differential response to ocean acidification in physiological traits of Concholepas concholepas populations

    Science.gov (United States)

    Lardies, Marco A.; Arias, María Belén; Poupin, María Josefina; Manríquez, Patricio H.; Torres, Rodrigo; Vargas, Cristian A.; Navarro, Jorge M.; Lagos, Nelson A.

    2014-07-01

    Phenotypic adaptation to environmental fluctuations frequently occurs by preexisting plasticity and its role as a major component of variation in physiological diversity is being widely recognized. Few studies have considered the change in phenotypic flexibility among geographic populations in marine calcifiers to ocean acidification projections, despite the fact that this type of study provides understanding about how the organism may respond to this chemical change in the ocean. We examined the geographic variation in CO2 seawater concentrations in the phenotype and in the reaction norm of physiological traits using a laboratory mesocosm approach with short-term acclimation in two contrasting populations (Antofagasta and Calfuco) of the intertidal snail Concholepas concholepas. Our results show that elevated pCO2 conditions increase standard metabolic rates in both populations of the snail juveniles, likely due to the higher energy cost of homeostasis. Juveniles of C. concholepas in the Calfuco (southern) population showed a lower increment of metabolic rate in high-pCO2 environments concordant with a lesser gene expression of a heat shock protein with respect to the Antofagasta (northern) population. Combined these results indicate a negative effect of ocean acidification on whole-organism functioning of C. concholepas. Finally, the significant Population × pCO2 level interaction in both studied traits indicates that there is variation between populations in response to high-pCO2 conditions.

  16. Population differentiation and genetic diversity of Trichophyton rubrum as revealed by highly discriminatory microsatellites.

    Science.gov (United States)

    Gong, Jie; Wu, Weiwei; Ran, MengLong; Wang, Xiaowen; Liu, Wei; Wan, Zhe; Yao, Limin; Li, Ruoyu

    2016-10-01

    Little is known regarding the population information of Trichophyton rubrum due to a lack of strains with clear sampling information and molecular markers with high discriminatory power. In the present study, we developed a set of microsatellite markers that have a cumulative discriminatory power was 0.993. Using these microsatellites loci, 243 strains T. rubrum that had clear sampling information were analysed. Three genetic diversity indices (Shannon's Information Index, Nei's unbiased gene diversity and allelic richness) were shown to be related to the human population size of the sampling city rather than mean annual temperature or humidity. Population structure analyses revealed that T. rubrum can be separated into two clusters. AMOVA results indicated that genetic variation was more significant between these two clusters than among geographical populations. Our work is the first to reveal population information of T. rubrum using highly discriminatory molecular markers, and suggest that T. rubrum populations in cities with larger population size might have better adaptability due to higher genetic diversity under selective pressures (such as antifungal agents). Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Label-free detection of neuronal differentiation in cell populations using high-throughput live-cell imaging of PC12 cells.

    Directory of Open Access Journals (Sweden)

    Sebastian Weber

    Full Text Available Detection of neuronal cell differentiation is essential to study cell fate decisions under various stimuli and/or environmental conditions. Many tools exist that quantify differentiation by neurite length measurements of single cells. However, quantification of differentiation in whole cell populations remains elusive so far. Because such populations can consist of both proliferating and differentiating cells, the task to assess the overall differentiation status is not trivial and requires a high-throughput, fully automated approach to analyze sufficient data for a statistically significant discrimination to determine cell differentiation. We address the problem of detecting differentiation in a mixed population of proliferating and differentiating cells over time by supervised classification. Using nerve growth factor induced differentiation of PC12 cells, we monitor the changes in cell morphology over 6 days by phase-contrast live-cell imaging. For general applicability, the classification procedure starts out with many features to identify those that maximize discrimination of differentiated and undifferentiated cells and to eliminate features sensitive to systematic measurement artifacts. The resulting image analysis determines the optimal post treatment day for training and achieves a near perfect classification of differentiation, which we confirmed in technically and biologically independent as well as differently designed experiments. Our approach allows to monitor neuronal cell populations repeatedly over days without any interference. It requires only an initial calibration and training step and is thereafter capable to discriminate further experiments. In conclusion, this enables long-term, large-scale studies of cell populations with minimized costs and efforts for detecting effects of external manipulation of neuronal cell differentiation.

  18. Development of microsatellite markers to genetically differentiate populations of Octopus minor from Korea and China.

    Science.gov (United States)

    Kang, Jung-Ha; Kim, Yi-Kyung; Park, Jung-Youn; An, Chel-Min; Jun, Je-Chun

    2012-08-01

    Of the more than 300 octopus species, Octopus minor is one of the most popular and economically important species in Eastern Asia, including Korea, along with O. vulgaris, O. ocellatus, and O. aegina. We developed 19 microsatellite markers from Octopus minor and eight polymorphic markers were developed to analyze the genetic diversity and relationships among four octopus populations from Korea and three from China. The number of alleles per locus varied from 10 to 49, and allelic richness per locus ranged from 2 to 16.4 across all populations. The average allele number among the populations was 11.1, with a minimum of 8.3 and a maximum of 13.6. The mean allelic richness was 8.7 in all populations. The Hardy-Weinberg equilibrium (HWE) test revealed significant deviation in 19 of the 56 single-locus sites, and null alleles were presumed in five of eight loci. The pairwise F ( ST ) values between populations from Korea and China differed significantly in all pairwise comparisons. The genetic distances between the China and Korea samples ranged from 0.161 to 0.454. The genetic distances among the populations from Korea ranged from 0.033 to 0.090, with an average of 0.062; those among populations from China ranged from 0.191 to 0.316, with an average of 0.254. The populations from Korea and China formed clearly separated into clusters via an unweighted pair group method with arithmetic mean dendrogram. Furthermore, a population from muddy flats on the western coast of the Korean Peninsula and one from a rocky area on Jeju Island formed clearly separated subclusters. An assignment test based on the allele distribution discriminated between the Korean and Chinese origins with 96.9 % accuracy.

  19. Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia.

    Science.gov (United States)

    Balanovsky, O; Chukhryaeva, M; Zaporozhchenko, V; Urasin, V; Zhabagin, M; Hovhannisyan, A; Agdzhoyan, A; Dibirova, K; Kuznetsova, M; Koshel, S; Pocheshkhova, E; Alborova, I; Skhalyakho, R; Utevska, O; Mustafin, Kh; Yepiskoposyan, L; Tyler-Smith, C; Balanovska, E

    2017-04-01

    Y-chromosomal variation in West Asian populations has so far been studied in less detail than in the neighboring Europe. Here, we analyzed 598 Y-chromosomes from two West Asian subregions-Transcaucasia and the Armenian plateau-using 40 Y-SNPs and 17 Y-STRs and combined them with previously published data from the region. The West Asian populations fell into two clusters: upland populations from the Anatolian, Armenian and Iranian plateaus, and lowland populations from the Levant, Mesopotamia and the Arabian Peninsula. This geographic subdivision corresponds with the linguistic difference between Indo-European and Turkic speakers, on the one hand, and Semitic speakers, on the other. This subdivision could be traced back to the Neolithic epoch, when upland populations from the Anatolian and Iranian plateaus carried similar haplogroup spectra but did not overlap with lowland populations from the Levant. We also found that the initial gene pool of the Armenian motherland population has been well preserved in most groups of the Armenian Diaspora. In view of the contribution of West Asians to the autosomal gene pool of the steppe Yamnaya archaeological culture, we sequenced a large portion of the Y-chromosome in haplogroup R1b samples from present-day East European steppe populations. The ancient Yamnaya samples are located on the "eastern" R-GG400 branch of haplogroup R1b-L23, showing that the paternal descendants of the Yamnaya still live in the Pontic steppe and that the ancient Yamnaya population was not an important source of paternal lineages in present-day West Europeans.

  20. Mutational meltdown in laboratory yeast populations

    NARCIS (Netherlands)

    Zeyl, C.; Mizesko, M.; Visser, de J.A.G.M.

    2001-01-01

    In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because

  1. Differentiation between Carex arenaria L. populations at the eastern range margin based on female and male glumes variation

    Directory of Open Access Journals (Sweden)

    Lech Urbaniak

    2014-01-01

    Full Text Available 480 spikes from 16 populations of Carex arenaria L. planted in an experimental garden were collected and analysed for 4 female and 4 male glumes each. The characteristic of the interpopulational differentiation on the area of Poland was based on multivariate analysis, Student t-test and the coefficients of variation. The separateness of three populations from the isolated inland stations - 3(Góra, 11 (Tuczno, 15 (Poznań and individual character of - 2 (Wisełka, 6 (Sobieszewo from the coast and 9 (Ołobok from Lower Silesia is shown. The lowest level of variation and in consequence a particular usefulness for taxonomic considerations have two characters - a and a' (length of female and male glumes. The obtained pattern of interpopulational differentiation may be caused by various factors - migration routes on the Polish territory; selection pressures associated with different ecological conditions present in fixed dunes along the Baltic Sea coast and in isolated inland stations, occupied by C. arenaria; reduction of an extensive primary populations to markedly smaller isolated subpopulations.

  2. Genetic differentiation and history of populations of the Italian treefrog Hyla intermedia: lack of concordance between mitochondrial and nuclear markers.

    Science.gov (United States)

    Canestrelli, Daniele; Verardi, Andrea; Nascetti, Giuseppe

    2007-07-01

    The genetic differentiation among 33 populations of the Italian treefrog, Hyla intermedia (Anura: Hylidae), was investigated using both biparentally (23 allozyme loci) and maternally (partial mitochondrial cytochrome b gene) inherited markers. Two main population groups were evidenced by both markers, located north and south of the northern Apennines. However, the pattern of differentiation between these two groups was much less pronounced at allozymes than at mtDNA, leading to gene flow estimates that were 25 times lower at mitochondrial than at nuclear level. Also, the mtDNA divergence between the two groups was particularly marked for two cospecific lineages of anuran amphibians (the P-distance being on average 9.04%), while their average genetic distance at allozymes was comparatively low (D (NEI) = 0.07). This contrasting pattern of nuclear versus mitochondrial genetic variation is discussed in the context of: (1) marker specific selection, (2) secondary contact and sex-biased gene flow and (3) ancestral polymorphism and colonization from north to south. Finally we emphasize how, for population genetic studies, the use of multiple markers having distinct evolutionary properties can help unravel the existence of more complex evolutionary histories.

  3. Effect of estradiol on proliferation and differentiation of side population stem/progenitor cells from murine endometrium

    Directory of Open Access Journals (Sweden)

    Xu Jing

    2011-07-01

    Full Text Available Abstract Background In our previous study, endometrium side population cells (SP cells were isolated from postpartum murine uterus, and characterized by a heterogeneous population of stem/progenitor cells. In this study, we investigated the effect of estrogen on the proliferation and differentiation of SP cells. Methods SP and non-SP cells of postpartum murine endometrium were isolated by DNA dye Hoechst 33342. The expression of estrogen receptor 1 (ESR1 was measured by reverse transcription polymerase chain reaction (RT-PCR, Real-time PCR, Western blot, immunofluorescence and immunohistochemistry. The proliferation and differentiation of SP cells treated with different concentrations [10(-8 M-10(-6 M] of estradiol (E2 and E2+ ICI182780 (Faslodex, inhibitor of ESR1 were measured by 3-(4, 5-dimethylthiazoly1-2-2,5-diphenyltetrazolium bromide(MTT and clonogenic assays. Results (1 SP cells expressed ESR1 at a higher level than non-SP cells. (2 The level of E2 in the serum and the expression of ESR1 in the uterus of postpartum murine changed in the same manner with the ratio of SP cells to total uterus cells at a different postpartum time point. ESR1, as ABCG2 is also predominantly located in the stroma and the glandular epithelium of the uterus. (3 10(-6 M E2 notably promoted the proliferation of SP cells after treatment for 24 h. This effect could be inhibited by ICI182780. E2 at the concentration of 10(-7 M or 10(-8 M was sent to impair the large cloning efficiency (CE of SP cells. Conclusions The effect of estrogen on the proliferation and differentiation of endometrium SP cells via ESR1 was observed and it was in a concentration dependent fashion. Clearly, more work is needed to understand the in vivo effect of E2 at the physiological concentration on the differentiation of SP cells.

  4. Differential Impact of Tobacco Control Policies on Youth Sub-Populations

    OpenAIRE

    Tauras, John A.; Chaloupka, Frank J; Jidong Huang

    2013-01-01

    Background: While previous studies have demonstrated the efficacy of tobacco control interventions in reducing tobacco use among youth overall, there have been very few studies that examine the potential differential impact of tobacco control policies on various youth subgroups, defined by socio-economic status (SES), race/ethnicity, and gender. Objective: We examined the relationship between state-level cigarette prices and smoke-free air laws and youth smoking prevalence and intensity for v...

  5. Differential impact of tobacco control policies on youth sub-populations

    National Research Council Canada - National Science Library

    Tauras, John A; Huang, Jidong; Chaloupka, Frank J

    2013-01-01

    ...), race/ethnicity, and gender. We examined the relationship between state-level cigarette prices and smoke-free air laws and youth smoking prevalence and intensity for various youth sub-populations in the United States...

  6. Differential Migration between Discrete Populations of Juvenile Red-Tailed Hawks (Buteo jamaicensis)

    National Research Council Canada - National Science Library

    Joshua M. Hull; Holly B. Ernest; Jill A. Harley; Allen M. Fish; Angus C. Hull

    2009-01-01

    .... We used 24 years of banding data, 15 years of migration counts, and molecular genetic data from 17 microsatellite loci to describe the migration phenology, direction, and population connectivity of Red-tailed Hawks (Buteo jamaicensis...

  7. Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

    Directory of Open Access Journals (Sweden)

    Jian Li

    2009-11-01

    Full Text Available Although copy number variation (CNV has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip(R Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01. After merging overlapping CNVs, 1135 copy number variation regions (CNVRs, covering approximately 439 Mb (14.3% of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.

  8. [Genetic Differentiation of Populations of Baikal Endemic Sergentia baicalensis Tshern. (Diptera, Chironomidae)].

    Science.gov (United States)

    Kravtsova, L S; Bukin, Yu S; Peretolchina, T E; Shcherbakov, D Yu

    2015-07-01

    The population structure of endemic species Sergentia baicalensis (Diptera, Chironomidae) from Lake Baikal was studied using the first subunit of the cytochrome C oxidase mitochondrial gene (Col). Two populations inhabiting different basins of this lake, the southern-central and northern, were detected. It was confirmed that the divergence time of this species was dated to Late Miocene (9.53 ± 3.9 Mya), during the period when geographically separated basins existed in the Baikal rift zone.

  9. Differential susceptibility in steelhead trout populations to an emergent MD strain of infectious hematopoietic necrosis virus

    Science.gov (United States)

    Breyta, R.; Jones, Amelia; Kurath, Gael

    2014-01-01

    A significant emergence of trout-adapted MD subgroup infectious hematopoietic necrosis virus (IHNV) began in the coastal region of Washington State, USA, in 2007. This emergence event lasted until 2011 and caused both asymptomatic adult fish infection and symptomatic epidemic disease and mortality in juvenile fish. Incidence of virus during this emergence demonstrated a heterogeneous distribution among rivers of the coastal region, leaving fish populations of some rivers apparently untouched while others suffered significant and recurrent infection and mortality (Breyta et. al. 2013; Dis Aquat Org 104:179-195). In this study, we examined the possible contribution of variations in susceptibility of fish populations, age-related resistance, and virus virulence to the observed landscape heterogeneity. We found that the most significant variable was host susceptibility: by controlled experimental challenge studies steelhead trout populations with no history of IHNV infection were 1 to 3 orders of magnitude more sensitive than a fish population with a long history of IHNV infection. In addition, 2 fish populations from the same river, which descended relatively recently from a common ancestral population, demonstrated 1 to 2 orders of magnitude difference in susceptibility. Fish age-related development of resistance was most evident in the more susceptible of 2 related fish populations. Finally, the strain of virus involved in the 2007 coastal Washington emergence had high virulence but was within the range of other known M group viruses tested. These results suggest that one major driver of landscape heterogeneity in the 2007 coastal Washington IHNV emergence was variation in fish population susceptibility and that this trait may have a heritable component.

  10. Palatal rugae in population differentiation between South and North Indians: A discriminant function analysis.

    Science.gov (United States)

    Shanmugam, Shankar; Anuthama, Krishnamurthy; Shaikh, Hidayathulla; Murali, Kruthika; Suresan, Vinay; Nisharudeen, Khaja; Brinda Devi, Sulur Pechimuthu; Rajasundaram, Prakash

    2012-07-01

    The present study is aimed at delineation of different types of rugae in two different populations and developing a discriminant function for the same. A total of 940 subjects were included in the present study. The sample consisted of 466 subjects from South Indian population and 474 from North Indian population in the age group of 18-23 years. Neo colloid Easy flow((™)) alginate impressions of maxillary arch were made and casts were immediately poured with Type IV dental stone. A sharp graphite pencil was used to delineate the rugae and patterns were recorded according to the classification given by Kapali et al. The association between different population and different sexes was analyzed with chi-square test and a stepwise discriminant function analysis was also performed to develop a discriminant formula. Wavy, curved and straight rugae were the most common forms in both groups. Chi-square analysis for association between rugae shape and population groups showed significant differences among all the rugae patterns at the P analysis for assessing sex differences in the rugae shapes showed significant difference in straight, unification and circular type. Five rugae shapes - curved, wavy, nonspecific, unification and circular - were selected for discriminant function. The discriminant function equation obtained from the different rugae shapes in the present study was highly accurate enough to distinguish the Southern and Northern Indian population with the classification accuracy of 87.8%. Thus to identify a specific population, separate discriminant function formulae have to be developed. Hence, the study of palatal rugae is one of the simple and reliable tools for population identification in forensic science.

  11. Differential patterns of Batrachochytrium dendrobatidis infection in relict amphibian populations following severe disease-associated declines.

    Science.gov (United States)

    Whitfield, Steven M; Alvarado, Gilbert; Abarca, Juan; Zumbado, Hector; Zuñiga, Ibrahim; Wainwright, Mark; Kerby, Jacob

    2017-09-20

    Global amphibian biodiversity has declined dramatically in the past 4 decades, and many amphibian species have declined to near extinction as a result of emergence of the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd). However, persistent or recovering populations of several amphibian species have recently been rediscovered, and such populations may illustrate how amphibian species that are highly susceptible to chytridiomycosis may survive in the presence of Bd. We conducted field surveys for Bd infection in 7 species of Costa Rican amphibians (all species that have declined to near extinction but for which isolated populations persist) to characterize infection profiles in highly Bd-susceptible amphibians post-decline. We found highly variable patterns in infection, with some species showing low prevalence (~10%) and low infection intensity and others showing high infection prevalence (>80%) and either low or high infection intensity. Across sites, infection rates were negatively associated with mean annual precipitation, and infection intensity across sites was negatively associated with mean average temperatures. Our results illustrate that even the most Bd-susceptible amphibians can persist in Bd-enzootic ecosystems, and that multiple ecological or evolutionary mechanisms likely exist for host-pathogen co-existence between Bd and the most Bd-susceptible amphibian species. Continued monitoring of these populations is necessary to evaluate population trends (continuing decline, stability, or population growth). These results should inform efforts to mitigate impacts of Bd on amphibians in the field.

  12. Epidemiologic differentiation of diagnostic and screening populations for the assessment of cervical dysplasia using optical technologies.

    Science.gov (United States)

    Pham, Bryan; Rhodes, Helen; Milbourne, Andrea; Adler-Storthz, Karen; Follen, Michele; Scheurer, Michael E

    2012-02-01

    We report here the logistic modeling of the epidemiologic differences between a diagnostic population and a screening population recruited for the study of optical technologies for cervical cancer detection. The goal of this analysis was to determine if there were differences in the sociodemographic or clinical factors between subjects recruited to our diagnostic and screening trials. Epidemiologic data were obtained from a risk factor interview as a component of a multicenter Phase II clinical trial that used fluorescence and reflectance point spectroscopy to diagnose cervical disease. Participants with recent or past abnormal findings on a Papanicolaou smear were grouped into the diagnostic (high-risk) population, whereas those with a history of normal findings on Papanicolaou smears and no cervical treatments were grouped into the screening (low-risk) population. Our model revealed that nonwhite race, higher than a high school education, and peri- and postmenopausal status were associated with the screening population. A history of genital infections, current oral contraceptive use, human papillomavirus positivity (by Hybrid Capture II and consensus polymerase chain reaction), and worst histological diagnosis at clinic visit were important predictors of being in the diagnostic group. We were successful in recruiting 2 distinctive populations and anticipate being able to use these results to more correctly classify women at higher risk for cervical lesions in our future studies of optical spectroscopy. Copyright © 2012 Elsevier HS Journals, Inc. All rights reserved.

  13. Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

    KAUST Repository

    Banguera-Hinestroza, E.

    2014-02-27

    Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact. © 2014 Springer Science+Business Media Dordrecht.

  14. Leaf n-alkanes as characters differentiating coastal and continental Juniperus deltoides populations from the Balkan Peninsula.

    Science.gov (United States)

    Rajčević, Nemanja; Janaćković, Pedja; Dodoš, Tanja; Tešević, Vele; Bojović, Srdjan; Marin, Petar D

    2014-07-01

    The composition of the cuticular n-alkanes isolated from the leaves of nine populations of Juniperus deltoides R.P.Adams from continental and coastal areas of the Balkan Peninsula was characterized by GC-FID and GC/MS analyses. In the leaf waxes, 14 n-alkane homologues with chain-lengths ranging from C22 to C35 were identified. n-Tritriacontane (C33 ) was dominant in the waxes of all populations, but variations between the populations in the contents of all n-alkanes were observed. Several statistical methods (ANOVA, principal component, discriminant, and cluster analyses) were used to investigate the diversity and variability of the cuticular-leaf-n-alkane patterns of the nine J. deltoides populations. This is the first report on the n-alkane composition for this species. The multivariate statistical analyses evidenced a high correlation of the leaf-n-alkane pattern with the geographical distribution of the investigated samples, differentiating the coastal from the continental populations of this taxon. Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

  15. Behavioral, ecological and genetic differentiation in an open environment--a study of a mysid population in the Baltic Sea.

    Directory of Open Access Journals (Sweden)

    Martin Ogonowski

    Full Text Available Diel vertical migration (DVM is often assumed to encompass an entire population. However, bimodal nighttime vertical distributions have been observed in various taxa. Mysid shrimp populations also display this pattern with one group concentrated in the pelagia and the other near the bottom. This may indicate alternative migratory strategies, resembling the seasonal partial migrations seen in birds, fishes and amphibians, where only a subset of the population migrates. To assess the persistence of these alternative strategies, we analyzed the nitrogen and carbon stable isotope signatures (as proxies for diet, biochemical indices (as proxies for growth condition, and genetic population divergence in the Baltic mysid Mysis salemaai collected at night in the pelagia and close to the bottom. Stable isotope signatures were significantly different between migrants (pelagic samples and residents (benthic samples, indicating persistent diet differences, with pelagic mysids having a more uniform and carnivorous diet. Sequencing of the mitochondrial cytochrome subunit I (COI gene showed genetic differentiation attributable to geographic location but not between benthic and pelagic groups. Divergent migration strategies were however supported by significantly lower gene flow between benthic populations indicating that these groups have a lower predisposition for horizontal migrations compared to pelagic ones. Different migration strategies did not convey measurable growth benefits as pelagic and benthic mysids had similar growth condition indices. Thus, the combination of ecological, biochemical and genetic markers indicate that this partial migration may be a plastic behavioral trait that yields equal growth benefits.

  16. Development and application of microsatellites in Carcinus maenas: genetic differentiation between Northern and Central Portuguese populations.

    Directory of Open Access Journals (Sweden)

    Sónia Pascoal

    Full Text Available Carcinus maenas, the common shore crab of European coastal waters, has recently gained notoriety due to its globally invasive nature associated with drastic ecological and economic effects. The native ubiquity and worldwide importance of C. maenas has resulted in it becoming one of the best-studied estuarine crustacean species globally. Accordingly, there is significant interest in investigating the population genetic structure of this broadly distributed crab along European and invaded coastlines. Here, we developed polymerase chain reaction (PCR primers for one dinucleotide and two trinucleotide microsatellite loci, resulting from an enrichment process based on Portuguese populations. Combining these three new markers with six existing markers, we examined levels of genetic diversity and population structure of C. maenas in two coastal regions from Northern and Central Portugal. Genotypes showed that locus polymorphism ranged from 10 to 42 alleles (N = 135 and observed heterozygosity per locus ranged from 0.745 to 0.987 with expected heterozygosity ranging from 0.711 to 0.960; values typical of marine decapods. The markers revealed weak, but significant structuring among populations (global F(ST = 0.004 across a 450 km (over-water distance spatial scale. Combinations of these and existing markers will be useful for studying population genetic parameters at a range of spatial scales of C. maenas throughout its expanding species range.

  17. Genetic Differentiations among the Populations of Salvia japonica (Lamiaceae and Its Related Species

    Directory of Open Access Journals (Sweden)

    SUDARMONO

    2008-03-01

    Full Text Available Morphological and genetic variations within Salvia japonica (Lamiaceae and its related species in Japan were analyzed for clarifying their taxonomic significance. The genetic variations were explored through chloroplast and nuclear ribosomal DNA sequences and allozyme polymorphisms. Since chromosome numbers characterized the genus of Salvia, we also examined whether the karyotypes were different. We examined 58 populations of S. japonica and 14 populations of others species of Salvia. Among the populations of S. japonica represented four forms (f. japonica, f. longipes, f. lanuginosa and f. albiflora. The size of chromosomes were various among Salvia spp. Based on the allozyme as well as the DNA sequence, the populations of S. japonica separated from the others Salvia species. The populations of S. japonica exhibited four combinations of the morphological characters. However, these combinations did not correlate to the four forms of S. japonica. In addition, the morphological variations did not correlate to the allozyme and DNA sequences. It is suggested that the four morphological variations as well as the four form of S. japonica should not considered to be a taxonomic unit; accordingly, S. japonica were considered to be still at the early stage of speciation process.

  18. Kangaroo mother care: a multi-country analysis of health system bottlenecks and potential solutions.

    Science.gov (United States)

    Vesel, Linda; Bergh, Anne-Marie; Kerber, Kate J; Valsangkar, Bina; Mazia, Goldy; Moxon, Sarah G; Blencowe, Hannah; Darmstadt, Gary L; de Graft Johnson, Joseph; Dickson, Kim E; Ruiz Peláez, Juan; von Xylander, Severin; Lawn, Joy E

    2015-01-01

    Preterm birth is now the leading cause of under-five child deaths worldwide with one million direct deaths plus approximately another million where preterm is a risk factor for neonatal deaths due to other causes. There is strong evidence that kangaroo mother care (KMC) reduces mortality among babies with birth weight methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for KMC. Marked differences were found in the perceived severity of health system bottlenecks between Asian and African countries, with the former reporting more significant or very major bottlenecks for KMC with respect to all the health system building blocks. Community ownership and health financing bottlenecks were significant or very major bottlenecks for KMC in both low and high mortality contexts, particularly in South Asia. Significant bottlenecks were also reported for leadership and governance and health workforce building blocks. There are at least a dozen countries worldwide with national KMC programmes, and we identify three pathways to scale: (1) champion-led; (2) project-initiated; and (3) health systems designed. The combination of all three pathways may lead to more rapid scale-up. KMC has the potential to save lives, and change the face of facility-based newborn care, whilst empowering women to care for their preterm newborns.

  19. The impact of share wave elastography in differentiation of hepatic hemangioma from malignant liver tumors in pediatric population

    Energy Technology Data Exchange (ETDEWEB)

    Özmen, Evrim, E-mail: evrimkilicdr@gmail.com [Department of Radiology, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Adaletli, İbrahim, E-mail: iadaletli@yahoo.com [Department of Radiology, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Kayadibi, Yasemin, E-mail: ysmnkurdoglu@gmail.com [Department of Radiology, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Emre, Şenol, E-mail: senolemre@hotmail.com [Department of Pediatric Surgery, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Kılıç, Fahrettin, E-mail: fahrettinkilic@hotmail.com [Department of Radiology, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Dervişoğlu, Sergülen, E-mail: selozmen@gmail.com [Department of Pathology, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Kuruğoğlu, Sebuh, E-mail: sebuhk@yahoo.com [Department of Radiology, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey); Şenyüz, Osman Faruk, E-mail: ofsenyuz@gmail.com [Department of Pediatric Surgery, Cerrahpasa Medical Faculty, Istanbul University, 34300, Kocamustafapasa, Istanbul (Turkey)

    2014-09-15

    Highlights: • We evaluated the impact of share wave elastography technique in differentiation hepatic hemangiomas from malignant liver tumors in pediatric population. • Share wave technique can increase the diagnostic capability of conventional ultrasonography in the differential diagnosis of liver tumors in children. • Share wave elastography is a potential adjunctive diagnostic technique for pediatric liver tumors. - Abstract: Objective: In children it is crucial to differentiate malignant liver tumors from the most common benign tumor, hepatic hemangiomas since the treatment strategies are quite different. We aimed to evaluate the efficiency of shear wave elastography (SWE) technique in differentiation of malignant hepatic tumors and hepatic hemangiomas. Methods: Twenty patients with hepatic tumor were included in our study. Two radiologists performed SWE for 13 patients with malignant hepatic tumors including hepatoblastoma (n = 7), hepatocellular carcinoma (n = 3), metastasis (n = 2), embryonal sarcoma (n = 1) and 7 patients with hepatic hemangioma. All of our patients were between the age of 1 and 192 months (mean age: 56.88 months). Receiver operating characteristic analysis was achieved to evaluate the diagnostic accuracy of SWE and to determine the optimal cut-off value in differentiation hepatic hemangioma from malignant hepatic tumors. Results: The mean SWE values (in kPa) for the first observer were 46.94 (13.8–145) and 22.38 (6.6–49.6) and those for the second observer were 57.91 (11–237) and 23.87 (6.4–57.5), respectively for malignant hepatic tumors and hepatic hemangiomas. The SWE values of malignant hepatic tumors were significantly higher than those of hepatic hemangioma (p = 0.02). The inter-observer agreement was almost perfect (0.81). The area under the receiver operating characteristic curve of SWE for differentiating the hepatic hemangioma from malignant hepatic tumors was 0.77 with a sensitivity of 72.7% and a specificity of 66

  20. Maladaptive behavior reinforces a recruitment bottleneck in newly settled fishes.

    Science.gov (United States)

    Fuiman, Lee A; Meekan, Mark G; McCormick, Mark I

    2010-09-01

    Settlement from the plankton ends the major dispersive stage of life for many marine organisms and exposes them to intense predation pressure in juvenile habitats. This predation mortality represents a life-history bottleneck that can determine recruitment success. At the level of individual predator-prey interactions, prey survival depends upon behavior, specifically how behavior affects prey conspicuousness and evasive ability. We conducted an experiment to identify behavioral traits and performance levels that are important determinants of which individuals survive or die soon after settlement. We measured a suite of behavioral traits on late stage, pre-settlement Ward's damsel (Pomacentrus wardi) collected using light traps. These behavioral traits included two measures of routine swimming (indicators of conspicuousness) and eight measures of escape performance to a visual startle stimulus. Fish were then released onto individual patch reefs, where divers measured an additional behavioral trait (boldness). We censused each patch reef until approximately 50% of the fish were missing (~24 h), which we assumed to be a result of predation. We used classification tree analysis to discriminate survivors from fish presumed dead based on poor behavioral performance. The classification tree revealed that individuals displaying the maladaptive combination of low escape response speed, low boldness on the reef, and high routine swimming speed were highly susceptible to predation (92.4% with this combination died within 24 h). This accounted for 55.2% of all fish that died. Several combinations of behavioral traits predicted likely survival over 24 h, but there was greater uncertainty about that prediction than there was for fish that were predicted to die. Thus maladaptive behavioral traits were easier to identify than adaptive traits.

  1. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Directory of Open Access Journals (Sweden)

    Thais C de Oliveira

    2017-07-01

    Full Text Available The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences, Peru (PER, n = 23, Colombia (COL, n = 31, and Mexico (MEX, n = 19.We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4 as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092. Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically

  2. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

    Directory of Open Access Journals (Sweden)

    Thomas Meredith M

    2009-10-01

    Full Text Available Abstract Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity

  3. A call for differentiated approaches to delivering HIV services to key populations

    Directory of Open Access Journals (Sweden)

    Virginia Macdonald

    2017-07-01

    Conclusions: The application of a differentiated service approach for KP could increase the number of people who know their status and receive effective and sustained prevention and treatment for HIV. However, while community-based and lay provider testing are effective and affordable, they are not implemented to scale. Furthermore regulatory barriers to legitimizing lay and peer providers as part of healthcare delivery systems need to be overcome in many settings. WHO recommendations on task shifting and decentralization of ART treatment and care are often not applied to KP settings.

  4. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic......The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed...... to be strongly philopatric and to form large aggregations that remain within separate home ranges with little interchange between units, but the level of differentiation within the species is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequence data...

  5. A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity.

    Science.gov (United States)

    Balding, D J; Nichols, R A

    1995-01-01

    A method is proposed for allowing for the effects of population differentiation, and other factors, in forensic inference based on DNA profiles. Much current forensic practice ignores, for example, the effects of coancestry and inappropriate databases and is consequently systematically biased against defendants. Problems with the 'product rule' for forensic identification have been highlighted by several authors, but important aspects of the problems are not widely appreciated. This arises in part because the match probability has often been confused with the relative frequency of the profile. Further, the analogous problems in paternity cases have received little attention. The proposed method is derived under general assumptions about the underlying population genetic processes. Probabilities relevant to forensic inference are expressed in terms of a single parameter whose values can be chosen to reflect the specific circumstances. The method is currently used in some UK courts and has important advantages over the 'Ceiling Principle' method, which has been criticized on a number of grounds.

  6. Damage to white matter bottlenecks contributes to language impairments after left hemispheric stroke.

    Science.gov (United States)

    Griffis, Joseph C; Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

    2017-01-01

    Damage to the white matter underlying the left posterior temporal lobe leads to deficits in multiple language functions. The posterior temporal white matter may correspond to a bottleneck where both dorsal and ventral language pathways are vulnerable to simultaneous damage. Damage to a second putative white matter bottleneck in the left deep prefrontal white matter involving projections associated with ventral language pathways and thalamo-cortical projections has recently been proposed as a source of semantic deficits after stroke. Here, we first used white matter atlases to identify the previously described white matter bottlenecks in the posterior temporal and deep prefrontal white matter. We then assessed the effects of damage to each region on measures of verbal fluency, picture naming, and auditory semantic decision-making in 43 chronic left hemispheric stroke patients. Damage to the posterior temporal bottleneck predicted deficits on all tasks, while damage to the anterior bottleneck only significantly predicted deficits in verbal fluency. Importantly, the effects of damage to the bottleneck regions were not attributable to lesion volume, lesion loads on the tracts traversing the bottlenecks, or damage to nearby cortical language areas. Multivariate lesion-symptom mapping revealed additional lesion predictors of deficits. Post-hoc fiber tracking of the peak white matter lesion predictors using a publicly available tractography atlas revealed evidence consistent with the results of the bottleneck analyses. Together, our results provide support for the proposal that spatially specific white matter damage affecting bottleneck regions, particularly in the posterior temporal lobe, contributes to chronic language deficits after left hemispheric stroke. This may reflect the simultaneous disruption of signaling in dorsal and ventral language processing streams.

  7. Differences in Strength and Timing of the mtDNA Bottleneck between Zebrafish Germline and Non-germline Cells

    Directory of Open Access Journals (Sweden)

    Auke B.C. Otten

    2016-07-01

    Full Text Available We studied the mtDNA bottleneck in zebrafish to elucidate size, timing, and variation in germline and non-germline cells. Mature zebrafish oocytes contain, on average, 19.0 × 106 mtDNA molecules with high variation between oocytes. During embryogenesis, the mtDNA copy number decreases to ∼170 mtDNA molecules per primordial germ cell (PGC, a number similar to that in mammals, and to ∼50 per non-PGC. These occur at the same developmental stage, implying considerable variation in mtDNA copy number in (non-PGCs of the same female, dictated by variation in the mature oocyte. The presence of oocytes with low mtDNA numbers, if similar in humans, could explain how (de novo mutations can reach high mutation loads within a single generation. High mtDNA copy numbers in mature oocytes are established by mtDNA replication during oocyte development. Bottleneck differences between germline and non-germline cells, due to early differentiation of PGCs, may account for different distribution patterns of familial mutations.

  8. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.

    Science.gov (United States)

    Fernandes, Andrew D; Macklaim, Jean M; Linn, Thomas G; Reid, Gregor; Gloor, Gregory B

    2013-01-01

    Experimental variance is a major challenge when dealing with high-throughput sequencing data. This variance has several sources: sampling replication, technical replication, variability within biological conditions, and variability between biological conditions. The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these categories as per standard ANOVA models. We show that the partitioning of within-condition to between-condition variation cannot reasonably be ignored, whether in single-organism RNA-Seq or in Meta-RNA-Seq experiments, and further find that commonly-used RNA-Seq analysis tools, as described in the literature, do not enforce the constraint that the sum of relative expression levels must be one, and thus report expression levels that are systematically distorted. These two factors lead to misleading inferences if not properly accommodated. As it is usually only the biological between-condition and within-condition differences that are of interest, we developed ALDEx, an ANOVA-like differential expression procedure, to identify genes with greater between- to within-condition differences. We show that the presence of differential expression and the magnitude of these comparative differences can be reasonably estimated with even very small sample sizes.

  9. Microscopic theory of spatial-temporal congested traffic patterns at highway bottlenecks

    Science.gov (United States)

    Kerner, Boris S.; Klenov, Sergey L.

    2003-09-01

    A microscopic theory of spatial-temporal congested traffic patterns at highway bottlenecks due to on-ramps, merge bottlenecks (a reduction of highway lanes), and off-ramps is presented. The basic postulate of three-phase traffic theory is used, which claims that homogeneous (in space and time) model solutions (steady states) of synchronized flow cover a two dimensional region in the flow-density plane [B. S. Kerner, Phys. Rev. Lett. 81, 3797 (1998); Trans. Res. Rec. 1678, 160 (1999)]. Phase transitions leading to diverse congested patterns, pattern evolution, and pattern nonlinear features have been found. Diagrams of congested patterns, i.e., regions of the pattern emergence dependent on traffic demand, have been derived. Diverse effects of metastability with respect to the pattern formation have been found. The microscopic theory allows us to explain the main empirical pattern features at on-ramps and off-ramps which have recently been found [B. S. Kerner, Phys. Rev. E 65, 046138 (2002)]. (i) Rather than moving jams, synchronized flow first occurs at bottlenecks if the flow rate is slowly increasing. Wide moving jams can spontaneously occur only in synchronized flow. (ii) General patterns (GP) and synchronized flow patterns (SP) can spontaneously emerge at the bottlenecks. There can be the widening SP (WSP), the moving SP (MSP), and the localized SP. (iii) At on-ramps cases of “weak” and “strong” congestion should be distinguished. In contrast to weak congestion, under strong congestion the flow rate in synchronized flow in GP reaches a limit flow rate, the frequency of the moving jam emergence reaches a maximum, i.e., the GP characteristics under strong congestion do not depend on traffic demand. (iv) At the off-ramp GP with weak congestion occur. (v) A study of the pattern formation on a highway with two bottlenecks shows that diverse expanded patterns can occur, which cover both bottlenecks. SP first emerged at the downstream bottleneck can be caught

  10. Where are the polyps? Molecular identification, distribution and population differentiation of

    NARCIS (Netherlands)

    van Walraven, L.; Driessen, F.; van Bleijswijk, J.; Bol, A.; Luttikhuizen, P.C.; Coolen, J.; Bos, O.G.; Gittenberger, A.; Schrieken, N.; Langenberg, V.T.; van der Veer, H.W.

    2016-01-01

    For many species of metagenic jellyfish the location of the benthic polyps is unknown. To gain insight in the distribution, species composition and population structure of scyphozoan jellyfish polyps in the southern North Sea area, polyp samples were collected from natural and artificial substrates

  11. ISSR markers show differentiation among Italian populations of Asparagus acutifolius L

    Directory of Open Access Journals (Sweden)

    Gaudio Luciano

    2005-03-01

    Full Text Available Abstract Background Asparagus acutifolius L. is a dioecious and native plant species, widely distributed in the Mediterranean Basin. It is known for its fine flavour and could represent an important resource for cultivation programs in desert areas. Few molecular studies have been performed on this species. In the present paper, the ISSR technique was employed to study genetic diversity in Italian A. acutifolius. Results Twenty-three primers produced a total of 228 polymorphic fragments used to evaluate genetic variation. FST (0.4561 and Theta B (0.4776 values indicate a wide genetic variation among the samples examined. The distance UPGMA tree grouped together the genotypes strictly according to their geographical origin, showing that each sample is genetically structured and can be considered a distinct population. AMOVA analysis further confirmed genetic structuring of the populations. Population-specific fragments were also detected. Conclusion The results suggest that ISSR markers are useful in distinguishing the populations of A. acutifolius according to geographical origin, and confirm the importance of genetic studies for designing germplasm conservation strategies.

  12. ISSR markers show differentiation among Italian populations of Asparagus acutifolius L.

    Science.gov (United States)

    Sica, Maria; Gamba, Graziella; Montieri, Stefania; Gaudio, Luciano; Aceto, Serena

    2005-03-18

    Asparagus acutifolius L. is a dioecious and native plant species, widely distributed in the Mediterranean Basin. It is known for its fine flavour and could represent an important resource for cultivation programs in desert areas. Few molecular studies have been performed on this species. In the present paper, the ISSR technique was employed to study genetic diversity in Italian A. acutifolius. Twenty-three primers produced a total of 228 polymorphic fragments used to evaluate genetic variation. FST (0.4561) and Theta B (0.4776) values indicate a wide genetic variation among the samples examined. The distance UPGMA tree grouped together the genotypes strictly according to their geographical origin, showing that each sample is genetically structured and can be considered a distinct population. AMOVA analysis further confirmed genetic structuring of the populations. Population-specific fragments were also detected. The results suggest that ISSR markers are useful in distinguishing the populations of A. acutifolius according to geographical origin, and confirm the importance of genetic studies for designing germplasm conservation strategies.

  13. North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L.

    NARCIS (Netherlands)

    Olsen, JL; Stam, WT; Coyer, JA; Reusch, TBH; Billingham, M; Bostrom, C; Calvert, E; Christie, H; Granger, S; La Lumiere, R; Milchakova, N; Oudot-Le Secq, MP; Procaccini, G; Sanjabi, B; Serrao, E; Veldsink, J; Widdicombe, S; Wyllie-Echeverria, S

    As the most widespread seagrass in temperate waters of the Northern Hemisphere, Zostera marina provides a unique opportunity to investigate the extent to which the historical legacy of the last glacial maximum (LGM18000-10000 years BP) is detectable in modern population genetic structure. We used

  14. Evaluating sample allocation and effort in detecting population differentiation for discrete and continuously distributed individuals

    Science.gov (United States)

    Erin L. Landguth; Michael K. Schwartz

    2014-01-01

    One of the most pressing issues in spatial genetics concerns sampling. Traditionally, substructure and gene flow are estimated for individuals sampled within discrete populations. Because many species may be continuously distributed across a landscape without discrete boundaries, understanding sampling issues becomes paramount. Given large-scale, geographically broad...

  15. Spatial differentiation of population development in a declining region: the case of Saarland

    NARCIS (Netherlands)

    Hoekveld, J.J.

    2015-01-01

    We increasingly understand the causes of urban population decline: these can be, among others, processes of deindustrialisation, decreasing fertility or the succession of a city through the stages of urban life as the city matures. However, we are still insufficiently able to explain why differences

  16. Population genetic differentiation of height and body mass index across Europe

    DEFF Research Database (Denmark)

    Robinson, Matthew R.; Hemani, Gibran; Medina-Gomez, Carolina

    2015-01-01

    Across-nation differences in the mean values for complex traits are common(1-8), but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European coun...

  17. Genetic differentiation in life-history traits of introduced and native common ragweed (Ambrosia artemisiifolia) populations.

    Science.gov (United States)

    Hodgins, K A; Rieseberg, L

    2011-12-01

    Introduced species represent opportunities to observe evolution over contemporary time scales, and as exotics encounter new environments, adaptive responses can occur, potentially contributing to invasion. Here, we compare 22 native North American populations and 12 introduced European populations of common ragweed (Ambrosia artemisiifolia) in five common gardens (control, herbivory, light stress, nutrient stress and drought). We found evidence for improved growth and reproduction of the introduced populations in most environments, particularly in the light stress. However, under drought conditions, the introduced plants experienced more rapid wilting and mortality than their native counterparts, evidence consistent with a life-history trade-off between rapid growth and drought tolerance. Moreover, we found parallel latitudinal clines in flowering time and correlations between fitness components and the local climate of the source populations in both ranges. Together these data provide evidence for adaptation to local environmental conditions in the native and introduced range of common ragweed. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  18. Application of convolutional artificial neural networks to echocardiograms for differentiating congenital heart diseases in a pediatric population

    Science.gov (United States)

    Perrin, Douglas P.; Bueno, Alejandra; Rodriguez, Andrea; Marx, Gerald R.; del Nido, Pedro J.

    2017-03-01

    In this paper we describe a pilot study, where machine learning methods are used to differentiate between congenital heart diseases. Our approach was to apply convolutional neural networks (CNNs) to echocardiographic images from five different pediatric populations: normal, coarctation of the aorta (CoA), hypoplastic left heart syndrome (HLHS), transposition of the great arteries (TGA), and single ventricle (SV). We used a single network topology that was trained in a pairwise fashion in order to evaluate the potential to differentiate between patient populations. In total we used 59,151 echo frames drawn from 1,666 clinical sequences. Approximately 80% of the data was used for training, and the remainder for validation. Data was split at sequence boundaries to avoid having related images in the training and validation sets. While training was done with echo images/frames, evaluation was performed for both single frame discrimination as well as sequence discrimination (by majority voting). In total 10 networks were generated and evaluated. Unlike other domains where this network topology has been used, in ultrasound there is low visual variation between classes. This work shows the potential for CNNs to be applied to this low-variation domain of medical imaging for disease discrimination.

  19. The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland.

    Science.gov (United States)

    Mullins, Jacinta; McDevitt, Allan D; Kowalczyk, Rafał; Ruczyńska, Iwona; Górny, Marcin; Wójcik, Jan M

    2014-01-01

    The red fox ( Vulpes vulpes ) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002-2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.

  20. Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts.

    Directory of Open Access Journals (Sweden)

    Ericka R Havecker

    Full Text Available Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5' transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.

  1. Genetic, ecological, behavioral and geographic differentiation of populations in a thistle weevil: implications for speciation and biocontrol.

    Science.gov (United States)

    Olivieri, Isabelle; Singer, Michael C; Magalhães, Sara; Courtiol, Alexandre; Dubois, Yvain; Carbonell, David; Justy, Fabienne; Beldade, Patrícia; Parmesan, Camille; Michalakis, Yannis

    2008-02-01

    Because weevils are used as biocontrol agents against thistles, it is important to document and understand host shifts and the evolution of host-specificity in these insects. Furthermore, such host shifts are of fundamental interest to mechanisms of speciation. The mediterranean weevil Larinus cynarae normally parasitizes either one of two thistle genera, Onopordum and Cynara, being locally monophagous. In Sardinia, however, both host genera are used. We used three types of data to help understand this complex host use: (i) weevil attack rates on the two host genera among 53 different populations in Sardinia and nearby Corsica, (ii) host preference in a lab setting, and (iii) genetic (allozyme) differentiation among weevil populations exploiting the same or different hosts. Using a subset of populations from northern Sardinia, we attempted to relate interpopulation differences in host preference to gene flow among populations by comparing pairwise differences in oviposition preference (Qst) and in allozyme frequencies (Fst). Overall, Qst and Fst were positively correlated. Fst was positively correlated with geographic distance among pairs of populations using the same host, but not among different-host population pairs. As mating occurs on the hosts, this result suggests reinforcement. Genetic evidence indicates Cynara as the ancestral host of the weevils from both islands and our current studies suggest repeated attempts to colonize Onopordum, with a successful shift in Corsica and a partial shift in Sardinia. This scenario would explain why in Sardinia the level of attack was higher on Cynara than on Onopordum and why, when given a choice in the laboratory, Sardinian weevils preferred Cynara even when sampled from Onopordum. The lability of host shifts in L. cynarae supports caution in using these or related weevils as biocontrol agents of exotic thistles.

  2. Age and sex differentials in mortality during two nineteenth century population crises.

    Science.gov (United States)

    Pitkanen, K J; Mielke, J H

    1993-01-01

    "The exceptionally detailed Finnish materials are used to examine age- and sex-specific mortality in different regions during the country's last famine, the Great Famine of the 1860s. This is compared with another mortality crisis, the 1808-09 War. The results show that in cases when multiple infectious diseases were responsible for elevated mortality, the increases for different age categories were, by and large, proportional to the levels prevailing during normal times. However, excess mortality showed more variability for children. Furthermore, age- and sex-specific social behaviour (specifically large-scale temporary migration) during the crisis period shaped the age patterns and sex differentials in mortality." (SUMMARY IN FRE) excerpt

  3. Philopatry drives genetic differentiation in an island archipelago: comparative population genetics of Galapagos Nazca boobies (Sula granti) and great frigatebirds (Fregata minor).

    Science.gov (United States)

    Levin, Iris I; Parker, Patricia G

    2012-11-01

    Seabirds are considered highly mobile, able to fly great distances with few apparent barriers to dispersal. However, it is often the case that seabird populations exhibit strong population genetic structure despite their potential vagility. Here we show that Galapagos Nazca booby (Sula granti) populations are substantially differentiated, even within the small geographic scale of this archipelago. On the other hand, Galapagos great frigatebird (Fregata minor) populations do not show any genetic structure. We characterized the genetic differentiation by sampling five colonies of both species in the Galapagos archipelago and analyzing eight microsatellite loci and three mitochondrial genes. Using an F-statistic approach on the multilocus data, we found significant differentiation between nearly all island pairs of Nazca booby populations and a Bayesian clustering analysis provided support for three distinct genetic clusters. Mitochondrial DNA showed less differentiation of Nazca booby colonies; only Nazca boobies from the island of Darwin were significantly differentiated from individuals throughout the rest of the archipelago. Great frigatebird populations showed little to no evidence for genetic differentiation at the same scale. Only two island pairs (Darwin - Wolf, N. Seymour - Wolf) were significantly differentiated using the multilocus data, and only two island pairs had statistically significant φ(ST) values (N. Seymour - Darwin, N. Seymour - Wolf) according to the mitochondrial data. There was no significant pattern of isolation by distance for either species calculated using both markers. Seven of the ten Nazca booby migration rates calculated between island pairs were in the south or southeast to north or northwest direction. The population differentiation found among Galapagos Nazca booby colonies, but not great frigatebird colonies, is most likely due to differences in natal and breeding philopatry.

  4. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon

    DEFF Research Database (Denmark)

    Tartally, András; Kelager, Andreas; Fürst, Matthias Alois

    2016-01-01

    The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms...... on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow....

  5. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

    Directory of Open Access Journals (Sweden)

    Rodrick J Chiodini

    Full Text Available Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem

  6. Vitis Resistance to Pierce's Disease Is Characterized by Differential Xylella fastidiosa Populations in Stems and Leaves.

    Science.gov (United States)

    Krivanek, A F; Walker, M A

    2005-01-01

    ABSTRACT The pattern of Xylella fastidiosa infection in resistant and susceptible grapevines representing a diverse selection of Vitis spp. was characterized through measurements of X. fastidiosa bacterial movement and accumulation in artificially inoculated greenhouse-grown grapevines. A double-antibody sandwich enzyme-linked immunosorbent assay (ELISA) was optimized for quantification of X. fastidiosa populations and tested on known amounts of X. fastidiosa added to grape tissue extracts. Predicted versus known X. fastidiosa concentrations proved to be highly correlated (R(2) = 0.99). Populations of X. fastidiosa in stem internode, stem node, petiole, and leaf blade samples from the genotypes in this study were measured at 12 weeks postinoculation using the optimized ELISA procedure. Samples from each plant part were taken at eight positions along the inoculated shoots. Systemic infection was detected in both susceptible and resistant genotypes. Resistant genotypes were characterized by significant differences in X. fastidiosa populations between stem internodes and leaves (1.0 x 10(6) and 1.1 x 10(7) cells/g of sample, respectively). In contrast, the susceptible genotypes were characterized by high mean X. fastidiosa populations in both stems and leaves (5.6 x 10(7) and 4.8 x 10(7) cells/g, respectively) the latter of which were not significantly different from the resistant genotypes. A high correlation (R(2) = 0.97) between stem X. fastidiosa numbers to previously characterized field Pierce's disease (PD) performance indicates that the quantitative ELISA measurements of X. fastidiosa in greenhouse-grown grapevines should be a useful tool for predicting PD resistance under field conditions.

  7. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

    Science.gov (United States)

    Chiodini, Rodrick J.; Dowd, Scot E.; Chamberlin, William M.; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well reflected in the mucosa and/or downstream fecal material. PMID:26222621

  8. A novel approach to parasite population genetics: experimental infection reveals geographic differentiation, recombination and host-mediated population structure in Pasteuria ramosa, a bacterial parasite of Daphnia.

    Science.gov (United States)

    Andras, J P; Ebert, D

    2013-02-01

    The population structure of parasites is central to the ecology and evolution of host-parasite systems. Here, we investigate the population genetics of Pasteuria ramosa, a bacterial parasite of Daphnia. We used natural P. ramosa spore banks from the sediments of two geographically well-separated ponds to experimentally infect a panel of Daphnia magna host clones whose resistance phenotypes were previously known. In this way, we were able to assess the population structure of P. ramosa based on geography, host resistance phenotype and host genotype. Overall, genetic diversity of P. ramosa was high, and nearly all infected D. magna hosted more than one parasite haplotype. On the basis of the observation of recombinant haplotypes and relatively low levels of linkage disequilibrium, we conclude that P. ramosa engages in substantial recombination. Isolates were strongly differentiated by pond, indicating that gene flow is spatially restricted. Pasteuria ramosa isolates within one pond were segregated completely based on the resistance phenotype of the host-a result that, to our knowledge, has not been previously reported for a nonhuman parasite. To assess the comparability of experimental infections with natural P. ramosa isolates, we examined the population structure of naturally infected D. magna native to one of the two source ponds. We found that experimental and natural infections of the same host resistance phenotype from the same source pond were indistinguishable, indicating that experimental infections provide a means to representatively sample the diversity of P. ramosa while reducing the sampling bias often associated with studies of parasite epidemics. These results expand our knowledge of this model parasite, provide important context for the large existing body of research on this system and will guide the design of future studies of this host-parasite system. © 2012 Blackwell Publishing Ltd.

  9. Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos.

    Science.gov (United States)

    Gillingham, Mark A F; Béchet, Arnaud; Courtiol, Alexandre; Rendón-Martos, Manuel; Amat, Juan A; Samraoui, Boudjéma; Onmuş, Ortaç; Sommer, Simone; Cézilly, Frank

    2017-02-20

    Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity

  10. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

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    Carlos Sérgio Agostinho

    their proportions in the downriver stretch: fish samples in the ladder were clearly dominated by a few species, including some that do not need to be translocated. Thus, selectivity constitutes an important bottleneck to initiatives for translocating fish aimed at conserving their stocks or biodiversity. It is urgent to review the decision-making process for the construction of fish passages and to evaluate the functioning of those already operating.

  11. Processing bottlenecks in dual-task performance: structural limitation or strategic postponement?

    Science.gov (United States)

    Ruthruff, E.; Pashler, H. E.; Klaassen, A.

    2001-01-01

    Recent evidence indicates that a central bottleneck causes much of the slowing that occurs when two tasks are performed at the same time. This bottleneck might reflect a structural limitation inherent in the cognitive architecture. Alternatively, the bottleneck might reflect strategic (i.e., voluntary) postponement, induced by instructions to emphasize one task over the other. To distinguish structural limitations from strategic postponement, we examine a new paradigm in which subjects are told to place equal emphasis on both tasks and to emit both responses at about the same time. An experiment using this paradigm demonstrated patterns of interference that cannot easily be attributed to strategic postponement, preparation effects, or conflicts in response production. The data conform closely to the predictions of structural central bottleneck models.

  12. Culture, population structure, and low genetic diversity in Pleistocene hominins.

    Science.gov (United States)

    Premo, L S; Hublin, Jean-Jacques

    2009-01-06

    Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.

  13. Differential Estimates of Southern Flying Squirrel (Glaucomys volans) Population Structure Based on Capture Method.

    Energy Technology Data Exchange (ETDEWEB)

    Laves, Kevin S.; Loeb, Susan C.

    2006-01-01

    ABSTRACT.—It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucomys volans) using two methods to study their effect on red-cockaded woodpecker (Picoides borealis) reproductive success. Southern flying squirrels were captured at and removed from 30 red-cockaded woodpecker cluster sites during March to July 1994 and 1995 using Sherman traps placed in a grid encompassing a red-cockaded woodpecker nest tree and by hand from red-cockaded woodpecker cavities. Totals of 195 (1994) and 190 (1995) red-cockaded woodpecker cavities were examined at least three times each year. Trappability of southern flying squirrels in Sherman traps was significantly greater in 1995 (1.18%; 22,384 trap nights) than in 1994 (0.42%; 20,384 trap nights), and capture rate of southern flying squirrels in cavities was significantly greater in 1994 (22.7%; 502 cavity inspections) than in 1995 (10.8%; 555 cavity inspections). However, more southern flying squirrels were captured per cavity inspection than per Sherman trap night in both years. Male southern flying squirrels were more likely to be captured from cavities than in Sherman traps in 1994, but not in 1995. Both male and female juveniles were more likely to be captured in cavities than in traps in both years. In 1994 males in reproductive condition were more likely to be captured in cavities than in traps and in 1995 we captured significantly more reproductive females in cavities than in traps. Our data suggest that population estimates based solely on one trapping method may not represent true population size or structure of southern flying squirrels.

  14. [Differential expression of DTSsa4 Tc1-like transposons in closely related populations of Baikal ciscoes].

    Science.gov (United States)

    Bychenko, O S; Sukhanova, L V; Azhikina, T L; Sverdlov, E D

    2009-01-01

    Two representatives of Baikal ciscoes - lake cisco and omul - diverged from a common ancestor as recently as 10-20 thousand years ago. We have found an increasing expression level of DTSsa4 Tc1-like DNA transposons in cisco and omul brains. The mapping of the sequences of these transposons from Salmo salar and Danio rerio genomes has shown that in some cases, these transposons are located in the 5' and 3' regions, as well as in the promoter regions of various genes. Probably, Tc1-like transposons affect the activity of neighboring genes, providing the adaptive divergence of the cisco population.

  15. Assortative mating and differential male mating success in an ash hybrid zone population

    Directory of Open Access Journals (Sweden)

    Frascaria-Lacoste Nathalie

    2006-11-01

    Full Text Available Abstract Background The structure and evolution of hybrid zones depend mainly on the relative importance of dispersal and local adaptation, and on the strength of assortative mating. Here, we study the influence of dispersal, temporal isolation, variability in phenotypic traits and parasite attacks on the male mating success of two parental species and hybrids by real-time pollen flow analysis. We focus on a hybrid zone population between the two closely related ash species Fraxinus excelsior L. (common ash and F. angustifolia Vahl (narrow-leaved ash, which is composed of individuals of the two species and several hybrid types. This population is structured by flowering time: the F. excelsior individuals flower later than the F. angustifolia individuals, and the hybrid types flower in-between. Hybrids are scattered throughout the population, suggesting favorable conditions for their local adaptation. We estimate jointly the best-fitting dispersal kernel, the differences in male fecundity due to variation in phenotypic traits and level of parasite attack, and the strength of assortative mating due to differences in flowering phenology. In addition, we assess the effect of accounting for genotyping error on these estimations. Results We detected a very high pollen immigration rate and a fat-tailed dispersal kernel, counter-balanced by slight phenological assortative mating and short-distance pollen dispersal. Early intermediate flowering hybrids, which had the highest male mating success, showed optimal sex allocation and increased selfing rates. We detected asymmetry of gene flow, with early flowering trees participating more as pollen donors than late flowering trees. Conclusion This study provides striking evidence that long-distance gene flow alone is not sufficient to counter-act the effects of assortative mating and selfing. Phenological assortative mating and short-distance dispersal can create temporal and spatial structuring that appears

  16. On the Accurate Identification of Network Paths Having a Common Bottleneck

    Directory of Open Access Journals (Sweden)

    Muhammad Murtaza Yousaf

    2013-01-01

    Full Text Available We present a new mechanism for detecting shared bottlenecks between end-to-end paths in a network. Our mechanism, which only needs one-way delays from endpoints as an input, is based on the well-known linear algebraic approach: singular value decomposition (SVD. Clusters of flows which share a bottleneck are extracted from SVD results by applying an outlier detection method. Simulations with varying topologies and different network conditions show the high accuracy of our technique.

  17. Genetic Differentiation of Archachatina marginata Populations from Three Vegetation Zones Using Radom Amplified Polymorphic DNA Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Comfort O. AFOLAYAN

    2015-09-01

    Full Text Available The genetic differentiation of Archachatina marginata populations from three different zones of Nigeria was studied with a view to delimiting them into sub-species. One hundred and nineteen (119 snail specimens were collected, comprising of forty (40 specimens from Yenagoa (Mangrove forest and from Kabba (Guinea Savanna and thirty nine (39 specimens were from Ile-Ife (Rainforest. Eight parameters of the shell specimens of A. marginata which included height of shell, width of shell, aperture height, aperture width, spire length, spire width, penultimate whorl length and first whorl length were subjected to Principal Component Analysis (PCA and Canonical Variates Analysis (CVA to delimit the populations into sub-species. DNA of the various populations was extracted from the foot muscle using CTAB (Cetyl Trimethyl Ammonium Bromide method, which was subjected to RAPD analysis. The RAPD studies employed five (5 oligonucleotide primers (OPB – 17, OPH – 12, OPH – 17, OPI – 06 and OPU – 14 to amplify DNA from 27 samples of A. marginata selected. All five primers produced different band patterns, and the number of fragments amplified per primer varied. Among them, OPB- 17 gave DNA profiles with more numerous bands than the others primers. Both PCA and CVA produced overlapped clusters of A. marginata specimens from the three vegetation zones. The height of shell was observed to be the most variable feature and preferably the most suitable parameter for population grouping. Analysis of the proportions of polymorphic loci and band sharing based on similarity indices for A. marginata samples indicated a relatively high level of genetic variation in the populations from the three areas.

  18. Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

    Science.gov (United States)

    Jensen, Philip J; Fazio, Gennaro; Altman, Naomi; Praul, Craig; McNellis, Timothy W

    2014-04-04

    Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Gene expression profiling

  19. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks.

    Science.gov (United States)

    Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Claypool, Erin G; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y

    2013-01-01

    Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints.

  20. Variable temporo-insular cortex neuroanatomy in primates suggests a bottleneck effect in eastern gorillas

    Science.gov (United States)

    Barks, Sarah K.; Bauernfeind, Amy L.; Bonar, Christopher J.; Cranfield, Michael R.; de Sousa, Alexandra A.; Erwin, Joseph M.; Hopkins, William D.; Lewandowski, Albert H.; Mudakikwa, Antoine; Phillips, Kimberley A.; Raghanti, Mary Ann; Stimpson, Cheryl D.; Hof, Patrick R.; Zilles, Karl; Sherwood, Chet C.

    2013-01-01

    In this study, we describe an atypical neuroanatomical feature present in several primate species that involves a fusion between the temporal lobe (often including Heschl’s gyrus in great apes) and the posterior dorsal insula, such that a portion of insular cortex forms an isolated pocket medial to the Sylvian fissure. We assessed the frequency of this fusion in 56 primate species (including apes, Old World monkeys, New World monkeys, and strepsirrhines) using either magnetic resonance images or histological sections. A fusion between temporal cortex and posterior insula was present in 22 species (7 apes, 2 Old World monkeys, 4 New World monkeys, and 9 strepsirrhines). The temporo-insular fusion was observed in most eastern gorilla (Gorilla beringei beringei and G. b. graueri) specimens (62% and 100% of cases, respectively) but less frequently in other great apes and was never found in humans. We further explored the histology of this fusion in eastern gorillas by examining the cyto- and myeloarchitecture within this region, and observed that the degree to which deep cortical layers and white matter are incorporated into the fusion varies among individuals within a species. We suggest that fusion between temporal and insular cortex is an example of a relatively rare neuroanatomical feature that has become more common in eastern gorillas, possibly as the result of a population bottleneck effect. Characterizing the phylogenetic distribution of this morphology highlights a derived feature of these great apes. PMID:23939630

  1. Differential Vector Competency of Aedes albopictus Populations from the Americas for Zika Virus.

    Science.gov (United States)

    Azar, Sasha R; Roundy, Christopher M; Rossi, Shannan L; Huang, Jing H; Leal, Grace; Yun, Ruimei; Fernandez-Salas, Ildefonso; Vitek, Christopher J; Paploski, Igor A D; Stark, Pamela M; Vela, Jeremy; Debboun, Mustapha; Reyna, Martin; Kitron, Uriel; Ribeiro, Guilherme S; Hanley, Kathryn A; Vasilakis, Nikos; Weaver, Scott C

    2017-08-01

    To evaluate the potential role of Aedes albopictus (Skuse) as a vector of Zika virus (ZIKV), colonized mosquitoes of low generation number (≤ F5) from Brazil, Houston, and the Rio Grande Valley of Texas engorged on viremic mice infected with ZIKV strains originating from Senegal, Cambodia, Mexico, Brazil, or Puerto Rico. Vector competence was established by monitoring infection, dissemination, and transmission potential after 3, 7, and 14 days of extrinsic incubation. Positive saliva samples were assayed for infectious titer. Although all three mosquito populations were susceptible to all ZIKV strains, rates of infection, dissemination, and transmission differed among mosquito and virus strains. Aedes albopictus from Salvador, Brazil, were the least efficient vectors, demonstrating susceptibility to infection to two American strains of ZIKV but failing to shed virus in saliva. Mosquitoes from the Rio Grande Valley were the most efficient vectors and were capable of shedding all three tested ZIKV strains into saliva after 14 days of extrinsic incubation. In particular, ZIKV strain DakAR 41525 (Senegal 1954) was significantly more efficient at dissemination and saliva deposition than the others tested in Rio Grande mosquitoes. Overall, our data indicate that, while Ae. albopictus is capable of transmitting ZIKV, its competence is potentially dependent on geographic origin of both the mosquito population and the viral strain.

  2. Population density and structure drive differential investment in pre- and postmating sexual traits in frogs.

    Science.gov (United States)

    Lüpold, Stefan; Jin, Long; Liao, Wen Bo

    2017-06-01

    Sexual selection theory predicts a trade-off between premating (ornaments and armaments) and postmating (testes and ejaculates) sexual traits, assuming that growing and maintaining these traits is costly and that total reproductive investments are limited. The number of males in competition, the reproductive gains from investing in premating sexual traits, and the level of sperm competition are all predicted to influence how males allocate their finite resources to these traits. Yet, empirical examination of these predictions is currently scarce. Here, we studied relative expenditure on pre- and postmating sexual traits among frog species varying in their population density, operational sex ratio, and the number of competing males for each clutch of eggs. We found that the intensifying struggle to monopolize fertilizations as more and more males clasp the same female to fertilize her eggs shifts male reproductive investment toward sperm production and away from male weaponry. This shift, which is mediated by population density and the associated level of male-male competition, likely also explains the trade-off between pre- and postmating sexual traits in our much broader sample of anuran species. Our results highlight the power of such a multilevel approach in resolving the evolution of traits and allocation trade-offs. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  3. Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia.

    Science.gov (United States)

    Liu, Xuanyao; Yunus, Yushimah; Lu, Dongsheng; Aghakhanian, Farhang; Saw, Woei-Yuh; Deng, Lian; Ali, Mohammad; Wang, Xu; Nor, Fadzilah Mohd; Ghazali, Fadzilah; Rahman, Thuhairah Abdul; Shaari, Shahrul Azlin; Salleh, Mohd Zaki; Phipps, Maude E; Ong, Rick Twee-Hee; Xu, Shuhua; Teo, Yik-Ying; Hoh, Boon-Peng

    2015-04-01

    The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.

  4. Identification of production bottlenecks with the use of Plant Simulation software

    Directory of Open Access Journals (Sweden)

    Kikolski Mateusz

    2016-12-01

    Full Text Available The problem of bottlenecks is a key issue in optimising and increasing the efficiency of manufacturing processes. Detecting and analysing bottlenecks is one of the basic constraints to the contemporary production enterprises. The enterprises should not ignore problems that significantly influence the efficiency of the processes. People responsible for the proper course of production try to devise methods to eliminate bottlenecks and the waiting time at the production line. The possibilities of production lines are limited by the throughput of bottlenecks that disturb the smoothness of the processes. The presented results of the experimental research show the possibilities of a computer simulation as a method for analysing problems connected with limiting the production capacity. A computer-assisted simulation allows for studying issues of various complexities that could be too work-consuming or impossible while using classic analytical methods. The article presents the results of the computer model analysis that involved the functioning of machinery within a chosen technological line of an enterprise from a sanitary sector. The major objective of the paper is to identify the possibility of applying selected simulation tool while analysing production bottlenecks. An additional purpose is to illustrate the subjects of production bottlenecks and creating simulation models. The problem analysis involved the application of the software Tecnomatix Plant Simulation by Siemens. The basic methods of research used in the study were literature studies and computer simulation.

  5. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.

    Directory of Open Access Journals (Sweden)

    Haiyuan Yu

    2007-04-01

    Full Text Available It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has been on highly connected proteins ("hubs". As a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many "shortest paths" going through them, analogous to major bridges and tunnels on a highway map. Bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. In particular, they are more likely to be essential proteins. In fact, in regulatory and other directed networks, betweenness (i.e., "bottleneck-ness" is a much more significant indicator of essentiality than degree (i.e., "hub-ness". Furthermore, bottlenecks correspond to the dynamic components of the interaction network-they are significantly less well coexpressed with their neighbors than non-bottlenecks, implying that expression dynamics is wired into the network topology.

  6. Low genetic diversity and strong but shallow population differentiation suggests genetic homogenization by metapopulation dynamics in a social spider.

    Science.gov (United States)

    Settepani, V; Bechsgaard, J; Bilde, T

    2014-12-01

    Mating systems and population dynamics influence genetic diversity and structure. Species that experience inbreeding and limited gene flow are expected to evolve isolated, divergent genetic lineages. Metapopulation dynamics with frequent extinctions and colonizations may, on the other hand, deplete and homogenize genetic variation, if extinction rate is sufficiently high compared to the effect of drift in local demes. We investigated these theoretical predictions empirically in social spiders that are highly inbred. Social spiders show intranest mating, female-biased sex ratio, and frequent extinction and colonization events, factors that deplete genetic diversity within nests and populations and limit gene flow. We characterized population genetic structure in Stegodyphus sarasinorum, a social spider distributed across the Indian subcontinent. Species-wide genetic diversity was estimated over approximately 2800 km from Sri Lanka to Himalayas, by sequencing 16 protein-coding nuclear loci. We found 13 SNPs in 6592 bp (π = 0.00045) indicating low species-wide nucleotide diversity. Three genetic lineages were strongly differentiated; however, only one fixed difference among them suggests recent divergence. This is consistent with a scenario of metapopulation dynamics that homogenizes genetic diversity across the species' range. Ultimately, low standing genetic variation may hamper a species' ability to track environmental change and render social inbreeding spiders 'evolutionary dead-ends'. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  7. Physiological mechanism of population differentiation in shade-avoidance responses between woodland and clearing genotypes of Impatiens capensis.

    Science.gov (United States)

    von Wettberg, Eric J; Schmitt, Johanna

    2005-05-01

    Forest understory plants often respond less intensely to reduced ratios of red to far red (R : FR) light, an important signal of foliage shade, than conspecific or congeneric plants from open-canopy sites. Reduced responsiveness to low R : FR in plants from closed-canopy sites could be caused by two physiological mechanisms. First, closed-canopy plants could have less sensitive shade-avoidance responses to low R : FR. Second, the high irradiance response to FR (FR-HIR), which allows seedling de-etiolation under low R : FR, might be stronger or persist longer after de-etiolation in closed-canopy plants, thus counteracting shade-avoidance responses to low R : FR. These hypotheses were tested using diodes that emit red and far-red light to distinguish the responses to altered R : FR of genotypes of Impatiens capensis collected from a pair of open- and closed-canopy populations that have previously been shown to differ in sensitivity to R : FR. Genotypes from the open-canopy environment exhibited typical shade-avoidance responses, elongating in response to supplemental FR. However, genotypes from the closed-canopy environment responded to supplemental FR by elongating less than under ambient control conditions, indicating a persistent FR-HIR. Thus, the observed population differentiation in response to low R : FR may be linked to population differences in FR-HIR.

  8. Sex-differentiated migration patterns, protandry and phenology in North European songbird populations

    DEFF Research Database (Denmark)

    Tøttrup, Anders Peter; Thorup, Kasper

    2008-01-01

    This study aims to investigate causes and mechanisms controlling protandrous migration patterns (the earlier breeding area arrival of males relative to females) and inter-sexual differences in timing of migration in relation to the recent climate-driven changes in phenology. Using standardised...... with the largest change for the first arriving individuals. These findings seem in support of the "mate opportunity" hypothesis, as the arrival of males and females is strongly coupled and both sexes seem to compete for early arrival. Changes in timing of arrival in males and females as a response to climatic...... changes may influence subsequent mating decisions, with subsequent feedbacks on population dynamics such as reproductive success and individual fitness. However, during decades of consistent earlier spring arrival in all phases of migration we found no evidence of inter-sexual phenological differences....

  9. Larval Environment Alters Amphibian Immune Defenses Differentially across Life Stages and Populations.

    Directory of Open Access Journals (Sweden)

    Katherine L Krynak

    Full Text Available Recent global declines, extirpations and extinctions of wildlife caused by newly emergent diseases highlight the need to improve our knowledge of common environmental factors that affect the strength of immune defense traits. To achieve this goal, we examined the influence of acidification and shading of the larval environment on amphibian skin-associated innate immune defense traits, pre and post-metamorphosis, across two populations of American Bullfrogs (Rana catesbeiana, a species known for its wide-ranging environmental tolerance and introduced global distribution. We assessed treatment effects on 1 skin-associated microbial communities and 2 post-metamorphic antimicrobial peptide (AMP production and 3 AMP bioactivity against the fungal pathogen Batrachochytrium dendrobatidis (Bd. While habitat acidification did not affect survival, time to metamorphosis or juvenile mass, we found that a change in average pH from 7 to 6 caused a significant shift in the larval skin microbial community, an effect which disappeared after metamorphosis. Additionally, we found shifts in skin-associated microbial communities across life stages suggesting they are affected by the physiological or ecological changes associated with amphibian metamorphosis. Moreover, we found that post-metamorphic AMP production and bioactivity were significantly affected by the interactions between pH and shade treatments and interactive effects differed across populations. In contrast, there were no significant interactions between treatments on post-metamorphic microbial community structure suggesting that variation in AMPs did not affect microbial community structure within our study. Our findings indicate that commonly encountered variation in the larval environment (i.e. pond pH and degree of shading can have both immediate and long-term effects on the amphibian innate immune defense traits. Our work suggests that the susceptibility of amphibians to emerging diseases could be

  10. Differential effect of Agaricus host species on the population development of Megaselia halterata (Diptera: Phoridae).

    Science.gov (United States)

    Smith, J E; Challen, M P; White, P F; Edmondson, R N; Chandler, D

    2006-12-01

    Twelve isolates from the genus Agaricus (Fungi, Basidiomycota) were investigated for their ability to support development of the phorid fly, Megaselia halterata (Wood), which is an important pest of the commercial white button mushroom Agaricus bisporus. Combined effects of oviposition of adult female M. halterata and larval development in mushroom compost inoculated with Agaricus mycelium were determined using bioassays. The numbers of M. halterata offspring that developed were affected by the Agaricus isolate used, and there was a significant separation between resistant and susceptible isolates. In a bioassay where the female phorids had a choice of all 12 isolates for oviposition, three isolates produced >200 adults per 100 g compost pot while the remaining nine isolates had 100 adults per 100 g compost pot while the remainder resulted in <4 adults per pot. With the susceptible isolates, there was a positive correlation between increasing concentration of mycelium in the substrate and phorid development until the concentration exceeded 40% after which numbers of emerging phorids declined. Genetic identity of Agaricus isolates was determined using ITS sequencing and phylogenetic methods, which revealed two major cluster groups. Isolates supporting the development of large populations of M. halterata were located in one of these clusters (group I), and were either Agaricus bisporus or other species from the same Agaricus section Duploannulatae. Isolates that did not support the development of M. halterata populations were located in a different cluster (group II) and were more genetically distant from A. bisporus, e.g. Agaricus sections Arvenses, Minores and Xanthodermatei. Species of Agaricus with resistance to M. halterata could have significant potential for the breeding and cultivation of phorid-free mushrooms.

  11. Differentiation of functional constipation and constipation predominant irritable bowel syndrome based on Rome III criteria: a population-based study.

    Science.gov (United States)

    Koloski, N A; Jones, M; Young, M; Talley, N J

    2015-05-01

    While the Rome III classification recognises functional constipation (FC) and constipation predominant IBS (IBS-C) as distinct disorders, recent evidence has suggested that these disorders are difficult to separate in clinical practice. To identify whether clinical and lifestyle factors differentiate Rome III-defined IBS-C from FC based on gastrointestinal symptoms and lifestyle characteristics. 3260 people randomly selected from the Australian population returned a postal survey. FC and IBS-C were defined according to Rome III. The first model used logistic regression to differentiate IBS-C from FC based on lifestyle, quality-of-life and psychological characteristics. The second approach was data-driven employing latent class analysis (LCA) to identify naturally occurring clusters in the data considering all symptoms involved in the Rome III criteria for IBS-C and FC. We found n = 206 (6.5%; 95% CI 5.7-7.4%) people met strict Rome III FC whereas n = 109 (3.5%; 95% CI 2.8-4.1%) met strict Rome III IBS-C. The case-control approach indicated that FC patients reported an older age at onset of constipation, were less likely to exercise, had higher mental QoL and less health care seeking than IBS-C. LCA yielded one latent class that was predominantly (75%) FC, while the other class was approximately half IBS-C and half FC. The FC-dominated latent class had clearly lower levels of symptoms used to classify IBS (pain-related symptoms) and was more likely to be male (P = 0.046) but was otherwise similar in distribution of lifestyle factors to the mixed class. The latent class analysis approach suggests a differentiation based more on symptom severity rather than the Rome III view. © 2015 John Wiley & Sons Ltd.

  12. Epigenetic marks define the lineage and differentiation potential of two distinct neural crest-derived intermediate odontogenic progenitor populations.

    Science.gov (United States)

    Gopinathan, Gokul; Kolokythas, Antonia; Luan, Xianghong; Diekwisch, Thomas G H

    2013-06-15

    Epigenetic mechanisms, such as histone modifications, play an active role in the differentiation and lineage commitment of mesenchymal stem cells. In the present study, epigenetic states and differentiation profiles of two odontogenic neural crest-derived intermediate progenitor populations were compared: dental pulp (DP) and dental follicle (DF). ChIP on chip assays revealed substantial H3K27me3-mediated repression of odontoblast lineage genes DSPP and dentin matrix protein 1 (DMP1) in DF cells, but not in DP cells. Mineralization inductive conditions caused steep increases of mineralization and patterning gene expression levels in DP cells when compared to DF cells. In contrast, mineralization induction resulted in a highly dynamic histone modification response in DF cells, while there was only a subdued effect in DP cells. Both DF and DP progenitors featured H3K4me3-active marks on the promoters of early mineralization genes RUNX2, MSX2, and DLX5, while OSX, IBSP, and BGLAP promoters were enriched for H3K9me3 or H3K27me3. Compared to DF cells, DP cells expressed higher levels of three pluripotency-associated genes, OCT4, NANOG, and SOX2. Finally, gene ontology comparison of bivalent marks unique for DP and DF cells highlighted cell-cell attachment genes in DP cells and neurogenesis genes in DF cells. In conclusion, the present study indicates that the DF intermediate odontogenic neural crest lineage is distinguished from its DP counterpart by epigenetic repression of DSPP and DMP1 genes and through dynamic histone enrichment responses to mineralization induction. Findings presented here highlight the crucial role of epigenetic regulatory mechanisms in the terminal differentiation of odontogenic neural crest lineages.

  13. Ecotypic differentiation between urban and rural populations of the grasshopper Chorthippus brunneus relative to climate and habitat fragmentation.

    Science.gov (United States)

    San Martin Y Gomez, Gilles; Van Dyck, Hans

    2012-05-01

    Urbanization alters environmental conditions in multiple ways and offers an ecological or evolutionary challenge for organisms to cope with. Urban areas typically have a warmer climate and strongly fragmented herbaceous vegetation; the urban landscape matrix is often assumed to be hostile for many organisms. Here, we addressed the issue of evolutionary differentiation between urban and rural populations of an ectotherm insect, the grasshopper Chorthippus brunneus. We compared mobility-related morphology and climate-related life history traits measured on the first generation offspring of grasshoppers from urban and rural populations reared in a common garden laboratory experiment. We predicted (1) the urban phenotype to be more mobile (i.e., lower mass allocation to the abdomen, longer relative femur and wing lengths) than the rural phenotype; (2) the urban phenotype to be more warm adapted (e.g., higher female body mass); and (3) further evidence of local adaptation in the form of significant interaction effects between landscape of origin and breeding temperature. Both males and females of urban origin had significantly longer relative femur and wing lengths and lower mass allocation to the abdomen (i.e., higher investment in thorax and flight muscles) relative to individuals of rural origin. The results were overall significant but small (2-4%). Body mass and larval growth rate were much higher (+10%) in females of urban origin. For the life history traits, we did not find evidence for significant interaction effects between the landscape of origin and the two breeding temperatures. Our results point to ecotypic differentiation with urbanization for mobility-related morphology and climate-related life history traits. We argue that the warmer urban environment has an indirect effect through longer growth season rather than direct effects on the development.

  14. Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

    Directory of Open Access Journals (Sweden)

    Brunner Sylvia

    2008-05-01

    Full Text Available Abstract Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

  15. Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

    Science.gov (United States)

    Li, Fangting

    2017-01-01

    The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent

  16. Exploring differential item functioning in the SF-36 by demographic, clinical, psychological and social factors in an osteoarthritis population.

    Science.gov (United States)

    Pollard, Beth; Johnston, Marie; Dixon, Diane

    2013-12-11

    The SF-36 is a very commonly used generic measure of health outcome in osteoarthritis (OA). An important, but frequently overlooked, aspect of validating health outcome measures is to establish if items work in the same way across subgroup of a population. That is, if respondents have the same 'true' level of outcome, does the item give the same score in different subgroups or is it biased towards one subgroup or another. Differential item functioning (DIF) can identify items that may be biased for one group or another and has been applied to measuring patient reported outcomes. Items may show DIF for different conditions and between cultures, however the SF-36 has not been specifically examined in an osteoarthritis population nor in a UK population. Hence, the aim of the study was to apply the DIF method to the SF-36 for a UK OA population. The sample comprised a community sample of 763 people with OA who participated in the Somerset and Avon Survey of Health. The SF-36 was explored for DIF with respect to demographic, social, clinical and psychological factors. Well developed ordinal regression models were used to identify DIF items. DIF items were found by age (6 items), employment status (6 items), social class (2 items), mood (2 items), hip v knee (2 items), social deprivation (1 item) and body mass index (1 item). Although the impact of the DIF items rarely had a significant effect on the conclusions of group comparisons, in most cases there was a significant change in effect size. Overall, the SF-36 performed well with only a small number of DIF items identified, a reassuring finding in view of the frequent use of the SF-36 in OA. Nevertheless, where DIF items were identified it would be advisable to analyse data taking account of DIF items, especially when age effects are the focus of interest.

  17. The differential effects of increasing frequency and magnitude of extreme events on coral populations.

    Science.gov (United States)

    Fabina, Nicholas S; Baskett, Marissa L; Gross, Kevin

    2015-09-01

    Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additionally explored how coral traits and competition with macroalgae mediate changes in bleaching regimes. Our results predict that severe bleaching events reduce coral persistence more than frequent bleaching. Corals with low adult mortality and high growth rates are successful when bleaching is mild, but bleaching resistance is necessary to persist when bleaching is severe, regardless of frequency. The existence of macroalgae-dominated stable states reduces coral persistence and changes the relative importance of coral traits. Building on previous studies, our results predict that management efforts may need to prioritize protection of "weaker" corals with high adult mortality when bleaching is mild, and protection of "stronger" corals with high bleaching resistance when bleaching is severe. In summary, future reef projections and conservation targets depend on both local bleaching regimes and biodiversity.

  18. Differential expression of six genes and correlation with fatness traits in a unique broiler population

    Directory of Open Access Journals (Sweden)

    Pengcheng Jin

    2017-05-01

    Full Text Available Previous results from genome wide association studies (GWASs in chickens divergently selected for abdominal fat content of Northeast Agricultural University (NEAUHLF showed that many single nucleotide polymorphism (SNP variants were associated with abdominal fat content. Of them, six top significant SNPs at the genome level were located within SRD5A3, SGCZ, DLC1, GBE1, GALNT9 and DNAJB6 genes. Here, expression levels of these six candidate genes were investigated in abdominal fat and liver tissue between fat and lean broilers from the 14th generation population of NEAUHLF. The results showed that expression levels of SRD5A3, SGCZ and DNAJB6 in the abdominal fat and SRD5A3, DLC1, GALNT9, DNAJB6 and GBE1 in the liver tissue differed significantly between the fat and lean birds, and were correlated with abdominal fat traits. The findings will provide important references for further function investigation of the six candidate genes involved in abdominal fat deposition in chickens.

  19. Differential impacts of wildfire on the population dynamics of an old-forest species.

    Science.gov (United States)

    Rockweit, Jeremy T; Franklin, Alan B; Carlson, Peter C

    2017-06-01

    Ecological disturbances shape and maintain natural communities, but climate change and human land use can alter disturbance regimes and affect population persistence and vital rates in unpredictable ways. Species inhabiting landscapes shaped by wildfire have evolved mechanisms allowing them to persist under this dynamic disturbance type, which creates habitats of varying quality for these species. We utilized data from a 26-yr demographic study of northern spotted owls to analyze the influence of wildfire on apparent survival and recruitment rates. Wildfires occurred across different years and affected different spotted owl territories, which allowed us to implement a retrospective Before-After-Control-Impact (BACI) analysis and model the potential effect of wildfire extent and severity. Our results indicated that mixed-severity fires that burned at predominantly low-severity had little effect on survival and recruitment while fires characterized by more medium to high burn severities negatively affected spotted owl survival, with varying effects on recruitment. Reduced survival and increased recruitment rates on some territories affected by medium to high severity fires suggested that post-fire habitat quality was reduced resulting in territories that were marginally capable of supporting owls. We hypothesize these territories may have represented "sinks" that were supported by nearby "source" territories in a spatially heterogeneous landscape created by the mixed-severity fire regime of the region. © 2017 by the Ecological Society of America.

  20. Differential modulation of human intestinal bifidobacterium populations after consumption of a wild blueberry (Vaccinium angustifolium) drink.

    Science.gov (United States)

    Guglielmetti, Simone; Fracassetti, Daniela; Taverniti, Valentina; Del Bo', Cristian; Vendrame, Stefano; Klimis-Zacas, Dorothy; Arioli, Stefania; Riso, Patrizia; Porrini, Marisa

    2013-08-28

    Bifidobacteria are gaining increasing interest as health-promoting bacteria. Nonetheless, the genus comprises several species, which can exert different effects on human host. Previous studies showed that wild blueberry drink consumption could selectively increase intestinal bifidobacteria, suggesting an important role for the polyphenols and fiber present in wild blueberries. This study evaluated the modulation of the most common and abundant bifidobacterial taxonomic groups inhabiting the human gut in the same fecal samples. The analyses carried out showed that B. adolescentis, B. breve, B. catenulatum/pseudocatelulatum, and B. longum subsp. longum were always present in the group of subjects enrolled, whereas B. bifidum and B. longum subsp. infantis were not. Furthermore, it was found that the most predominant bifidobacterial species were B. longum subsp. longum and B. adolescentis. The results obtained revealed a high interindividual variability; however, a significant increase of B. longum subsp. infantis cell concentration was observed in the feces of volunteers after the wild blueberry drink treatment. This bifidobacterial group was shown to possess immunomodulatory abilities and to relieve symptoms and promote the regression of several gastrointestinal disorders. Thus, an increased cell concentration of B. longum subsp. infantis in the human gut could be considered of potential health benefit. In conclusion, wild blueberry consumption resulted in a specific bifidogenic effect that could positively affect certain populations of bifidobacteria with demonstrated health-promoting properties.

  1. Operculina from the northwestern Pacific (Sesoko Island, Japan) Species Differentiation, Population Dynamics, Growth and Development

    Science.gov (United States)

    Woeger, Julia; Eder, Wolfgang; Kinoshita, Shunichi; Briguglio, Antonino; Hohenegger, Johann

    2017-04-01

    During the last decades larger benthic foraminifera have gained importance as indicator species and are used in a variety of applications, from ecological monitoring, studying the effects of ocean acidification, or reconstructing paleoenvironments. They significantly contribute to the carbonate budget of costal areas and are invaluable tools in biostratigraphy. Even before their advancement as bioindicators, laboratory experiments have been conducted to investigate the effects of various ecological parameters on community composition, biology of single species, or investigating the effects of salinity and temperature on stable isotope composition of the foraminiferal test, to name only a few. The natural laboratory approach (continuous sampling over a period of more than one year) was conducted at the island of Sesoko (Okinawa, Japan). in combination with µ-CT scanning was used to reveal population dynamics of 3 different morphotypes of Operculina. The clarification of reproductive cycles as well as generation and size abundances were used to calculate natural growth models. Best fit was achieved using Bertalanffy and Michaelis-Menten functions. Exponential-, logistic-, generalized logistic-, Gompertz-function yielded weaker fits, when compared by coefficient of determination as well as Akaike Information criterion. The resulting growth curves and inferred growth rates were in turn used to evaluate the quality of a laboratory cultivation experiment carried out simultaneously over a period of 15 months. Culturing parameters such as temperature, light intensities, salinity and pH and light-dark duration were continuously adapted to measurements in the field. The average investigation time in culture was 77days. 13 Individuals lived more than 200 days, 3 reproduced asexually and one sexually. 14% of 186 Individuals were lost, while 22% could not be kept alive for more than one month. Growth curves also represent an instrumental source of information for the various

  2. Cryptic population structure in a large, mobile mammalian predator: the Scandinavian lynx.

    Science.gov (United States)

    Rueness, E K; Jorde, P E; Hellborg, L; Stenseth, N C; Ellegren, H; Jakobsen, K S

    2003-10-01

    The Eurasian lynx (Lynx lynx) is an example of a species that has gone through a severe bottleneck, leading to near extinction in Scandinavia around 1930-- a pattern shared with several other large carnivorous mammals. Here we extend previous genetic analyses of northern European lynx, confirming that lynx from the Scandinavian Peninsula represent a distinct clade differing clearly from European conspecifics. Furthermore, and despite a recent bottleneck and subsequent range expansion, we detect marked genetic differentiation within Scandinavia. This differentiation is largely manifested as a north-south gradient, with a linear increase in the quantity FST/(1 - FST). Aided by computer simulations we find that this pattern is unlikely to have arisen by random genetic drift in the short time since lynx started to expand in the 1950s, suggesting that the spatial structure may predate the bottleneck. Individual-based analyses indicate that, instead of a continuous gradient, Scandinavian lynx may be structured into three more or less distinct groups, possibly corresponding to northern, central and southern subpopulations. The presence of such structuring was unknown previously and was unexpected from general considerations on the mobility of the species, historical data and the absence of geographical barriers. Our study demonstrates how molecular markers may be used to detect cryptic population structure, invisible using traditional methods.

  3. Raptor mortality in wind farms of southern Spain: mitigation measures on a major migration bottleneck area

    Energy Technology Data Exchange (ETDEWEB)

    Gallego, Antonio-Roman Munoz; Lucas, Manuela De; Casado, Eva; Ferrer, Miguel

    2011-07-01

    Full text: To assess and monitor the impact of wind farms on fauna is crucial if we want to achieve ecologically sustainable development of this renewable energy resource. Today there are clear evidences that the probability of raptor collision depends critically on species behaviour and weather conditions, and the topographic factors related to each windmill. In our study area EIA were not able to predict this differential risk and in these circumstances mitigating the causes of bird mortality becomes a task of major importance, especially to those wind farms located in the Strait of Gibraltar, a water crossing of 14 km at its shortest distance acting as a major migration bottleneck for Paleo-African soaring migrants. We collected all available information on raptor collision from 1992, when the first wind farm was installed, and from 2005 until present a total of 262 turbines, grouped into 20 wind farms, were surveyed in a daily basis through a surveillance program with the main goal of register the actual mortality of birds. A total of 1291 raptors of 19 species were found of which 78.5% correspond to two species, the griffon vulture (Gyps fulvus) and the kestrel (Falco tinnunculus). In order to mitigate the impact on raptors, and particularly on the griffon vulture, in 2007 a program based on selective stopping of turbines was imposed, in collaboration with the environmental competent authority, on new approved projects. During 2008 there was a reduction in mortality by 48%, which remained in 2009 with a remarkably lower economic cost. An analysis of the temporal collision patterns will be presented and discussed, with special attention to those species suffering higher mortality rate, and to those who have some degree of threat. (Author)

  4. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Directory of Open Access Journals (Sweden)

    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  5. Thermodynamic modelling predicts energetic bottleneck for seabirds wintering in the northwest Atlantic.

    Science.gov (United States)

    Fort, Jérôme; Porter, Warren P; Grémillet, David

    2009-08-01

    Studying the energetics of marine top predators such as seabirds is essential to understand processes underlying adult winter survival and its impact on population dynamics. Winter survival is believed to be the single most important life-history trait in long-lived species but its determinants are largely unknown. Seabirds are inaccessible during this season, so conventional metabolic studies are extremely challenging and new approaches are needed. This paper describes and uses a state-of-the-art mechanistic model, Niche Mapper, to predict energy expenditure and food requirements of the two main seabird species wintering in the northwest Atlantic. We found that energy demand increased throughout the winter phase in both species. Across this period, mean estimated daily energy requirements were 1306 kJ day(-1) for Brünnich's guillemots (Uria lomvia) and 430 kJ day(-1) for little auks (Alle alle) wintering off Greenland and Newfoundland. Mean estimated daily food requirements were 547 g wet food day(-1) for Brünnich's guillemots, and 289 g wet food day(-1) for little auks. For both species and both wintering sites, our model predicts a sharp increase in energy expenditure between November and December, primarily driven by climatic factors such as air temperature and wind speed. These findings strongly suggest the existence of an energetic bottleneck for North Atlantic seabirds towards the end of the year, a challenging energetic phase which might explain recurrent events of winter mass-mortality, so called 'seabird winter wrecks'. Our study therefore emphasizes the relevance of thermodynamics/biophysical modelling for investigating the energy balance of wintering marine top predators and its interplay with survival and population dynamics in the context of global change.

  6. Central as well as peripheral attentional bottlenecks in dual-task performance activate lateral prefrontal cortices

    Directory of Open Access Journals (Sweden)

    Andre J Szameitat

    2016-03-01

    Full Text Available Human information processing suffers from severe limitations in parallel processing. In particular, when required to respond to two stimuli in rapid succession, processing bottlenecks may appear at central and peripheral stages of task processing. Importantly, it has been suggested that executive functions are needed to resolve the interference arising at such bottlenecks. The aims of the present study were to test whether central attentional limitations (i.e., bottleneck at the decisional response selection stage as well as peripheral limitations (i.e., bottleneck at response initiation both demand executive functions located in the lateral prefrontal cortex. For this, we re-analysed two previous studies, in which a total of 33 participants performed a dual-task according to the paradigm of the psychological refractory period (PRP during fMRI. In one study (N=17, the PRP task consisted of two two-choice response tasks known to suffer from a central bottleneck (CB group. In the other study (N=16, the PRP task consisted of two simple-response tasks known to suffer from a peripheral bottleneck (PB group. Both groups showed considerable dual-task costs in form of slowing of the second response in the dual-task (PRP effect. Imaging results are based on the subtraction of both single-tasks from the dual-task within each group. In the CB group, the bilateral middle frontal gyri and inferior frontal gyri were activated. Higher activation in these areas was associated with lower dual-task costs. In the PB group, the right middle frontal and inferior frontal gyrus were activated. Here, higher activation was associated with higher dual-task costs. In conclusion we suggest that central and peripheral bottlenecks both demand executive functions located in lateral prefrontal cortices. Differences between the CB and PB groups with respect to the exact prefrontal areas activated and the correlational patterns suggest that the executive functions resolving

  7. Whole-body MRI in generalized cystic lymphangiomatosis in the pediatric population: diagnosis, differential diagnoses, and follow-up

    Energy Technology Data Exchange (ETDEWEB)

    Herruela-Suffee, Cecile; Warin, Mathilde; Castier-Amouyel, Melody; Dallery, Florine; Bonnaire, Bruno; Constans, Jean-Marc [CHU Amiens-Picardie, Service de Radiologie, Amiens Cedex 1 (France)

    2016-02-15

    Generalized cystic lymphangiomatosis is a particularly rare disease with variable involvement of skeletal and extraskeletal sites. The key role of imaging in the diagnosis of this disease is no longer in doubt. The aim of our study was to demonstrate the contribution of whole-body magnetic resonance imaging (WB-MRI) at the diagnostic stage and during the follow-up in the pediatric population. Three children were included from 2008. The inclusion criteria were radiological images (conventional radiographs, computed tomography, and MRI) compatible with histological confirmation. Each child included received WB-MRI at the diagnosis stage and during follow-up. WB-MRI detected multiple hypointense T1 and hyperintense T2-STIR cystic bony lesions. One unnoticed mass in the retroperitoneum on computed tomography was easily detected by MRI. Mediastinal involvement was observed in one asymptomatic case. Histology was contributory in all cases. Preventive intramedullary nailings was done in one case. Follow-up WB-MRI detected new asymptomatic lesions in all cases. One child presented a third episode of lymphangitis of the right thigh during follow-up. Due to its high sensitivity to diagnose, ability to eliminate differential diagnoses and make exhaustive lesions assessment, and its non-radiating character for long-term follow-up, WB-MRI is highly recommended for generalized cystic lymphangiomatosis in the pediatric population. (orig.)

  8. Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy.

    Science.gov (United States)

    Nelson, Craig E; Carlson, Craig A; Ewart, Courtney S; Halewood, Elisa R

    2014-03-01

    Eddies are mesoscale oceanographic features (∼ 200 km diameter) that can cause transient blooms of phytoplankton by shifting density isoclines in relation to light and nutrient resources. To better understand how bacterioplankton respond to eddies, we examined depth-resolved distributions of bacterial populations across an anticyclonic mode-water eddy in the Sargasso Sea. Previous work on this eddy has documented elevated phytoplankton productivity and diatom abundance within the eddy centre with coincident bacterial productivity and biomass maxima. We illustrate bacterial community shifts within the eddy centre, differentiating populations uplifted along isopycnals from those enriched or depleted at horizons of enhanced bacterial and primary productivity. Phylotypes belonging to the Roseobacter, OCS116 and marine Actinobacteria clades were enriched in the eddy core and were highly correlated with pigment-based indicators of diatom abundance, supporting developing hypotheses that members of these clades associate with phytoplankton blooms. Typical mesopelagic clades (SAR202, SAR324, SAR406 and SAR11 IIb) were uplifted within the eddy centre, increasing bacterial diversity in the lower euphotic zone. Typical surface oligotrophic clades (SAR116, OM75, Prochlorococcus and SAR11 Ia) were relatively depleted in the eddy centre. The biogeochemical context of a bloom-inducing eddy provides insight into the ecology of the diverse uncultured bacterioplankton dominating the oligotrophic oceans. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  9. Local mate competition and transmission bottlenecks: a new model for understanding malaria parasite and other sex ratios.

    Science.gov (United States)

    Neal, Allison T; Taylor, Peter D

    2014-12-21

    The local mate competition model from sex ratio theory predicts female-biased sex ratios in populations that are highly subdivided during mating, and is thought to accord well with the population structure of malaria parasites. However, the selective advantage of female-biased sex ratios comes from the resulting increase in total reproductive output, an advantage the transmission biology of malaria parasite likely reduces. We develop a mathematical model to determine how bottlenecks in transmission that cause diminishing fitness returns from female production affect sex ratio evolution. We develop four variations of this model that incorporate whether or not parasite clones have the ability to detect others that occupy the same host and whether or not the number of clones affects the total mating population size. Our model indicates that transmission bottlenecks favor less female-biased sex ratios than those predicted under LMC. This effect is particularly pronounced if clones have no information about the presence of coexisting clones and the number of mating individuals per patch is fixed. The model could extend our understanding of malaria parasite sex ratios in three main ways. First, it identifies inconsistencies between the theoretical predictions and the data presented in a previous study, and proposes revised predictions that are more consistent with underlying biology of the parasite. Second, it may account for the positive association between parasite density and sex ratio observed within and between some species. Third, it predicts a relationship between mortality rates in the vector and sex ratios, which appears to be supported by the little existing data we have. While the inspiration for this model came from malaria parasites, it should apply to any system in which per capita dispersal success diminishes with increasing numbers of females in a patch. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia.

    Science.gov (United States)

    Wagner, Isaac D; Varghese, Litty B; Hemme, Christopher L; Wiegel, Juergen

    2013-01-01

    Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise F ST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an "epidemic" population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances.

  11. Glacial bottleneck and postglacial recolonization of a seed parasitic weevil, Curculio hilgendorfi, inferred from mitochondrial DNA variation.

    Science.gov (United States)

    Aoki, K; Kato, M; Murakami, N

    2008-07-01

    Climatic changes during glacial periods have had a major influence on the recent evolutionary history of living organisms, even in the warm temperate zone. We investigated phylogeographical patterns of a weevil Curculio hilgendorfi (Curculionidae), a host-specific seed predator of Castanopsis (Fagaceae) growing in the broadleaved evergreen forests in Japan. We examined 2709 bp of mitochondrial DNA for 204 individuals collected from 62 populations of the weevil. Four major haplogroups were detected, in southwestern and northeastern parts of the main islands and in central and southern parts of the Ryukyu Islands. The demographic population expansion was detected for the two groups in the main islands but not for the Ryukyu groups. The beginning time of the expansion was dated to 39,000-59,000 years ago, which is consistent with the end of the last glacial period. Our data also demonstrated that the southwestern population of the main islands has experienced a more severe bottleneck and more rapid population growth after glacial ages than the northeastern population. At least three refugial areas in the main islands were likely to have existed during the last glacial periods, one of which had not previously been recognized by analyses of intraspecific chloroplast DNA variation of several plant species growing in the broadleaved evergreen forests. Our results represent the first phylogeographical and population demographic analysis of an insect species associated with the broadleaved evergreen forests in Japan, and reveal more detailed postglacial history of the forests.

  12. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

    Science.gov (United States)

    Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

    2016-02-01

    The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

  13. Brown world forests: increased ungulate browsing keeps temperate trees in recruitment bottlenecks in resource hotspots.

    Science.gov (United States)

    Churski, Marcin; Bubnicki, Jakub W; Jędrzejewska, Bogumiła; Kuijper, Dries P J; Cromsigt, Joris P G M

    2017-04-01

    Plant biomass consumers (mammalian herbivory and fire) are increasingly seen as major drivers of ecosystem structure and function but the prevailing paradigm in temperate forest ecology is still that their dynamics are mainly bottom-up resource-controlled. Using conceptual advances from savanna ecology, particularly the demographic bottleneck model, we present a novel view on temperate forest dynamics that integrates consumer and resource control. We used a fully factorial experiment, with varying levels of ungulate herbivory and resource (light) availability, to investigate how these factors shape recruitment of five temperate tree species. We ran simulations to project how inter- and intraspecific differences in height increment under the different experimental scenarios influence long-term recruitment of tree species. Strong herbivore-driven demographic bottlenecks occurred in our temperate forest system, and bottlenecks were as strong under resource-rich as under resource-poor conditions. Increased browsing by herbivores in resource-rich patches strongly counteracted the increased escape strength of saplings in these patches. This finding is a crucial extension of the demographic bottleneck model which assumes that increased resource availability allows plants to more easily escape consumer-driven bottlenecks. Our study demonstrates that a more dynamic understanding of consumer-resource interactions is necessary, where consumers and plants both respond to resource availability. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  14. Study on traffic characteristics for a typical expressway on-ramp bottleneck considering various merging behaviors

    Science.gov (United States)

    Sun, Jie; Li, Zhipeng; Sun, Jian

    2015-12-01

    Recurring bottlenecks at freeway/expressway are considered as the main cause of traffic congestion in urban traffic system while on-ramp bottlenecks are the most significant sites that may result in congestion. In this paper, the traffic bottleneck characteristics for a simple and typical expressway on-ramp are investigated by the means of simulation modeling under the open boundary condition. In simulations, the running behaviors of each vehicle are described by a car-following model with a calibrated optimal velocity function, and lane changing actions at the merging section are modeled by a novel set of rules. We numerically derive the traffic volume of on-ramp bottleneck under different upstream arrival rates of mainline and ramp flows. It is found that the vehicles from the ramp strongly affect the pass of mainline vehicles and the merging ratio changes with the increasing of ramp vehicle, when the arrival rate of mainline flow is greater than a critical value. In addition, we clarify the dependence of the merging ratio of on-ramp bottleneck on the probability of lane changing and the length of the merging section, and some corresponding intelligent control strategies are proposed in actual traffic application.

  15. Differences in osmotolerance in freshwater and brackish water populations of Theodoxus fluviatilis (Gastropoda: Neritidae) are associated with differential protein expression.

    Science.gov (United States)

    Symanowski, Frauke; Hildebrandt, Jan-Peter

    2010-03-01

    The euryhaline gastropod Theodoxus fluviatilis is found in northern Germany in freshwater or in brackish water habitats in the Baltic Sea. Previous studies have revealed that individuals from both habitats are not distinguishable by morphological characters or by sequence comparison of DNA encoding 16S RNA or cytochrome C. As reported in this study, animals collected in the two habitats differ substantially in their physiological ability to adapt to different salinities. Comparison of accumulation rates of ninhydrin-positive substances (NPS) in foot muscle upon transfer of animals to higher medium salinities revealed that brackish water animals were perfectly able to mobilize NPS, while freshwater animals had only limited ability to do so. In an attempt to explore whether this difference in physiology may be caused by genetic differentiation, we compared protein expression patterns of soluble foot muscle proteins using 2D gel electrophoresis and silver staining. Of the 40 consistently detected protein spots, 27 showed similar levels in protein expression in animals collected from freshwater or brackish water habitats, respectively. In 12 spots, however, protein concentration was higher in brackish water than in freshwater animals. In four of these spots, expression levels followed increases or decreases in medium salinities. In a different set of 4 of these 12 spots, protein levels were always higher in brackish water as compared to freshwater animals, regardless of their physiological situation (14 days in artificial pond water or in medium with a salinity of 16 per thousand). The remaining 4 of the 12 spots had complex expression patterns. Protein levels of the remaining single spot were generally higher in freshwater animals than in brackish water animals. These expression patterns may indicate that freshwater and brackish water animals of T. fluviatilis belong to different locally adapted populations with subtle genetic differentiation.

  16. Childhood osteomyelitis-incidence and differentiation from other acute onset musculoskeletal features in a population-based study

    Science.gov (United States)

    Riise, Øystein Rolandsen; Kirkhus, Eva; Handeland, Kai Samson; Flatø, Berit; Reiseter, Tor; Cvancarova, Milada; Nakstad, Britt; Wathne, Karl-Olaf

    2008-01-01

    Background Osteomyelitis can be difficult to diagnose and there has previously not been a prospective approach to identify all children in a defined geographic area. The aim of this study was to assess the annual incidence of osteomyelitis in children, describe the patient and disease characteristics in those with acute (osteomyelitis (≥ 14 days disease duration), and differentiate osteomyelitis patients from those with other acute onset musculoskeletal features. Methods In a population-based Norwegian study physicians were asked to refer all children with suspected osteomyelitis. Children with osteomyelitis received follow-up at six weeks, six months and thereafter as long as clinically needed. Results The total annual incidence rate of osteomyelitis was 13 per 100 000 (acute osteomyelitis 8 and subacute osteomyelitis 5 per 100 000). The incidence was higher in patients under the age of 3 than in older children (OR 2.9, 95%: CI 2.3–3.7). The incidence of non-vertebral osteomyelitis was higher than the incidence of vertebral osteomyelitis (10 vs. 3 per 100 000; p = .002). Vertebral osteomyelitis was more frequent in girls than in boys (OR 7.0, 95%: CI 3.3–14.7). ESR ≥ 40 mm/hr had the highest positive predictive laboratory value to identify osteomyelitis patients at 26% and MRI had a positive predictive value of 85%. Long-bone infection was found in 16 (43%) patients. ESR, CRP, white blood cell count, neutrophils and platelet count were higher for patients with acute osteomyelitis than for patients with subacute osteomyelitis. Subacute findings on MRI and doctor's delay were more common in subacute osteomyelitis than in acute osteomyelitis patients. Blood culture was positive in 26% of the acute osteomyelitis patients and was negative in all the subacute osteomyelitis patients. Conclusion The annual incidence of osteomyelitis in Norway remains high. ESR values and MRI scan may help to identify osteomyelitis patients and differentiate acute and subacute

  17. Flows and Bottlenecks : Study of the physical flow of goods to and from the Region of Jönköping County and the possible bottlenecks

    OpenAIRE

    Öbrink, Anton; Kian, Leila

    2009-01-01

    A considerable amount of research has concentrated on the modes of transportation. Research has tended to focus on the growth and trends of the different modes of transportation on the national scale. Very little research has been undertaken into each region, and even less on those factors that prevent or act as barriers for transportation of goods in each region. Furthermore, very little research has been undertaken that examines the bottlenecks of the transportation flows in Jönköping. By i...

  18. Population Genetic Differentiation and Taxonomy of Three Closely Related Species of Saxifraga (Saxifragaceae from Southern Tibet and the Hengduan Mountains

    Directory of Open Access Journals (Sweden)

    Qing-Bo Gao

    2017-07-01

    Full Text Available The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G and the nuclear ribosomal DNA internal transcribed spacer (ITS were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S. pasumensis, and S. banmaensis. Chloroplast DNA (cpDNA phylogenies revealed two well supported clades, corresponding to S. umbellulata and S. pasumensis plus S. banmaensis. Topology of the ITS phylogeny was largely congruent with that generated from cpDNA haplotypes, but with minor conflicts which might be caused by incomplete lineage sorting. Analyses of molecular variance of both cpDNA and ITS datasets revealed that most variation was held between S. pasumensis s.l. (with S. banmaensis and S. umbellulata (92.31% for cpDNA; 69.78% for ITS, suggesting a high degree of genetic divergence between them. Molecular clock analysis based on ITS dataset suggested that the divergence between S. pasumensis s.l. and S. umbellulata can be dated to 8.50 Ma, probably a result of vicariant allopatric diversification associated with the uplift events of the HM. Vicariance associated with HM uplifts may also have been responsible for infraspecific differentiation in S. pasumensis. In contrast, infraspecific differentiation in S. umbellulata was most likely triggered by Quaternary glaciations. The much lower levels of gene diversity within populations of S. pasumensis compared with S. umbellulata could have resulted from both range contractions and human collection on account of its putative medicinal properties. Combining evidence from morphology, geographical distributions and

  19. Population Genetic Differentiation and Taxonomy of Three Closely Related Species of Saxifraga (Saxifragaceae) from Southern Tibet and the Hengduan Mountains.

    Science.gov (United States)

    Gao, Qing-Bo; Li, Yan; Gengji, Zhuo-Ma; Gornall, Richard J; Wang, Jiu-Li; Liu, Hai-Rui; Jia, Liu-Kun; Chen, Shi-Long

    2017-01-01

    The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S. pasumensis, and S. banmaensis. Chloroplast DNA (cpDNA) phylogenies revealed two well supported clades, corresponding to S. umbellulata and S. pasumensis plus S. banmaensis. Topology of the ITS phylogeny was largely congruent with that generated from cpDNA haplotypes, but with minor conflicts which might be caused by incomplete lineage sorting. Analyses of molecular variance of both cpDNA and ITS datasets revealed that most variation was held between S. pasumensis s.l. (with S. banmaensis) and S. umbellulata (92.31% for cpDNA; 69.78% for ITS), suggesting a high degree of genetic divergence between them. Molecular clock analysis based on ITS dataset suggested that the divergence between S. pasumensis s.l. and S. umbellulata can be dated to 8.50 Ma, probably a result of vicariant allopatric diversification associated with the uplift events of the HM. Vicariance associated with HM uplifts may also have been responsible for infraspecific differentiation in S. pasumensis. In contrast, infraspecific differentiation in S. umbellulata was most likely triggered by Quaternary glaciations. The much lower levels of gene diversity within populations of S. pasumensis compared with S. umbellulata could have resulted from both range contractions and human collection on account of its putative medicinal properties. Combining evidence from morphology, geographical distributions and molecular

  20. Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters.

    Science.gov (United States)

    Huang, Sui; Li, Fangting; Zhou, Joseph X; Qian, Hong

    2017-05-01

    The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN ) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and 'programmed', while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic 'blue-sky' bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent landscape

  1. Effects of speed bottleneck on traffic flow with feedback control signal

    Science.gov (United States)

    Zhu, Kangli; Bi, Jiantao; Wu, Jianjun; Li, Shubin

    2016-09-01

    Various car-following models (CMs) have been developed to capture the complex characteristics of microscopic traffic flow, among which the coupled map CM can better reveal and reflect various phenomena of practical traffic flow. Capacity change at bottleneck contributes to high-density traffic flow upstream the bottleneck and contains very complex dynamic behavior. In this paper, we analyze the effect of speed bottleneck on the spatial-temporal evolution characteristics of traffic flow, and propose a method to reduce traffic congestion with the feedback control signal based on CM. Simulation results highlight the potential of using the feedback signal to control the stop-and-go wave and furthermore to alleviate the traffic congestion effectively.

  2. IDENTIFYING BOTTLENECKS FOR APPROPRIATE INFANT FEEDING IN URBAN SLUMS, ALIGARH CITY.

    Directory of Open Access Journals (Sweden)

    Saira Mehnaz

    2012-04-01

    Full Text Available Introduction: Urban population is increasing rapidly. Majority of these families are poor or landless farmers and labourers, who settle down in peri-urban areas, creating slums. Urban slums are thus growing at an alarming rate. The present study was carried out with the general objective of identifying factors which prevent access to health services. Objectives: 1. To determine the prevalence of stunting, wasting, and underweight in infants and young children. 2. To determine presence of certain micro-environmental and socioeconomic factors associated with poor nutritional status of infants and children. Methodology: Baseline study was carried out in Oct –Nov 2009 (as a part of another ongoing study and data was collected in 110 Mothers who had delivered children during the last one month. In Oct 2010 these families were visited again the infants were followed up. 39 families had shifted to another location or emigrated back to their parent state or village mostly in search of seasonal employment as reported by neighbours. One family refused to cooperate. . Two infants had died. Remaining 68 Mothers were interviewed in friendly informal manner after taking consent for study. Results: (35.4% study subjects had migrated to other areas, as reported by neighbours. Of the 68 mothers interviewed during follow up visit, previous baseline record showed that a majority were 20-30 years of age. , only 2 mothers (2.9% had exclusively breastfed for 6 months. 46 (67.6% said they had not been contacted by any health worker during the last 3 months. All 68 children were malnourished. Immunization status was poor and 94.1% children had suffered from some illness in the last one month. Conclusion: Migration is a problem which makes it difficult for providers to give continuity of care. Capacity building of the community can reduce the the bottlenecks leading to marginalization and exclusion of slum mothers from the mainstream urban health services.

  3. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

    Science.gov (United States)

    Lockton, Steven; Ross-Ibarra, Jeffrey; Gaut, Brandon S.

    2008-01-01

    Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata. The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages. PMID:18772373

  4. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks.

    Science.gov (United States)

    Hughes, Joseph; Allen, Richard C; Baguelin, Marc; Hampson, Katie; Baillie, Gregory J; Elton, Debra; Newton, J Richard; Kellam, Paul; Wood, James L N; Holmes, Edward C; Murcia, Pablo R

    2012-12-01

    The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV) to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics.

  5. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks.

    Directory of Open Access Journals (Sweden)

    Joseph Hughes

    2012-12-01

    Full Text Available The ability of influenza A viruses (IAVs to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics.

  6. Budget process bottlenecks for immunization financing in the Democratic Republic of the Congo (DRC).

    Science.gov (United States)

    Le Gargasson, Jean-Bernard; Mibulumukini, Benoît; Gessner, Bradford D; Colombini, Anaïs

    2014-02-19

    In Democratic Republic of the Congo (DRC), the availability of domestic resources for the immunization program is limited and relies mostly on external donor support. DRC has introduced a series of reforms to move the country toward performance-based management and program budgets. The objectives of the study were to: (i) describe the budget process norm, (ii) analyze the budget process in practice and associated bottlenecks at each of its phases, and (iii) collect suggestions made by the actors involved to improve the situation. Quantitative and qualitative data were collected through: a review of published and gray literature, and individual interviews. Bottlenecks in the budget process and disbursement of funds for immunization are one of the causes of limited domestic resources for the program. Critical bottlenecks include: excessive use of off-budget procedures; limited human resources and capacity; lack of motivation; interference from ministries with the standard budget process; dependency toward the development partner's disbursements schedule; and lack of budget implementation tracking. Results show that the health sector's mobilization rate was 59% in 2011. For the credit line specific to immunization program activities, the mobilization rate for the national Expanded Program for Immunization (EPI) was 26% in 2011 and 43% for vaccines (2010). The main bottleneck for the EPI budget line (2011) and vaccine budget line (2011) occurs at the authorization phase. Budget process bottlenecks identified in the analysis lead to a low mobilization rate for the immunization program. The bottlenecks identified show that a poor flow of funds causes an insufficient percentage of already allocated resources to reach various health system levels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Populism

    OpenAIRE

    Abts, Koenraad; Van Kessel, Stijn

    2015-01-01

    Populism is a concept applied to a wide range of political movements and actors across the globe. There is, at the same time, considerable confusion about the attributes and manifestation of populism, as well as its impact on democracy. This contribution identifies the defining elements of the populist ideology and discusses the varieties in which populism manifests itself, for instance as a component of certain party families. We finally discuss various normative interpretations of populism,...

  8. Bone Marrow-Derived Stem Cell Populations Are Differentially Regulated by Thyroid or/and Ovarian Hormone Loss

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    Bassam F. Mogharbel

    2017-10-01

    Full Text Available Bone marrow-derived stem cells (BMDSCs play an essential role in organ repair and regeneration. The molecular mechanisms by which hormones control BMDSCs proliferation and differentiation are unclear. Our aim in this study was to investigate how a lack of ovarian or/and thyroid hormones affects stem cell number in bone marrow lineage. To examine the effect of thyroid or/and ovarian hormones on the proliferative activity of BMDSCs, we removed the thyroid or/and the ovaries of adult female rats. An absence of ovarian and thyroid hormones was confirmed by Pap staining and Thyroid Stimulating Hormone (TSH measurement, respectively. To obtain the stem cells from the bone marrow, we punctured the iliac crest, and aspirated and isolated cells by using a density gradient. Specific markers were used by cytometry to identify the different BMDSCs types: endothelial progenitor cells (EPCs, precursor B cells/pro-B cells, and mesenchymal stem cells (MSCs. Interestingly, our results showed that hypothyroidism caused a significant increase in the percentage of EPCs, whereas a lack of ovarian hormones significantly increased the precursor B cells/pro-B cells. Moreover, the removal of both glands led to increased MSCs. In conclusion, both ovarian and thyroid hormones appear to have key and diverse roles in regulating the proliferation of cells populations of the bone marrow.

  9. Differential association between circulating testosterone and infection risk by several viruses in natural cat populations: a behavioural-mediated effect?

    Science.gov (United States)

    Hellard, E; Fouchet, D; Rey, B; Mouchet, A; Poulet, H; Pontier, D

    2013-04-01

    Testosterone is involved in the development and expression of physiological, morphological and behavioural traits. High levels are often associated with high infection risk and/or intensity, suggesting a trade-off between sexual traits and immunity. Classically invoked mechanisms are immunological or behavioural, i.e., testosterone increases susceptibility or resistance to parasites via an impact on immunity or modulates behaviours involved in parasite transmission. However, studies report contrasted patterns. Given its modes of action and the diversity of host-parasite interactions, testosterone should not act similarly on all interactions. To reduce host and context diversity, we studied 3 viruses in the same cat population: the aggressively transmitted Feline Immunodeficiency virus (FIV), and the Feline Calicivirus (FCV) and Herpesvirus (FHV) both transmitted during friendly contacts. Testosterone had a strong effect on the probability of being positive to FIV whereas its effect was significantly weaker on FCV and FHV. These findings demonstrate that testosterone can be differentially associated with parasites of the same type (viruses). The difference we observed was consistent with a behavioural-mediated effect (increased aggressiveness), supporting the idea that the testosterone effect on infection risk is at least partially driven by behavioural mechanisms in our system. Further investigations (e.g., individual immunity measures) are required to confirm this hypothesis.

  10. Evidence for recent populations bottlenecks in northern spotted owls (Strix occidentalis Caurina)

    Science.gov (United States)

    W.Chris Funk; Eric D. Forsman; Matthew Johnson; Thomas D. Mullins; Susan M.. Haig

    2009-01-01

    The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the US Endangered Species Act. Despite protection of its remaining forest habitat, recent field studies show continued declines of northern spotted owls. One potential threat to northern spotted owls which has not yet been...

  11. Evolutionary Inferences from DNA Variation at the 6-Phosphogluconate Dehydrogenase Locus in Natural Populations of Drosophila: Selection and Geographic Differentiation

    Science.gov (United States)

    Begun, D. J.; Aquadro, C. F.

    1994-01-01

    observed extensive differences in the amount and distribution of variation in D. melanogaster Pgd samples from the United States and Zimbabwe which cannot be explained by differential selection on the Fast/Slow polymorphism in these two geographic regions. Thus, genetic drift among partially isolated populations has also been an important factor in determining the distribution of variation at Pgd in D. melanogaster. Finally, we assayed four-cutter variation at Pgd in a sample of 19 D. simulans X chromosomes and observed reduced levels of DNA variability and high levels of linkage disequilibrium. These patterns are consistent with predictions of some hitchhiking models. PMID:8138153

  12. Population genetic structure of an estuarine and a reef fish species exploited by Brazilian artisanal fishing

    Directory of Open Access Journals (Sweden)

    Regina H.G. Priolli

    2016-11-01

    Full Text Available In this study, we used microsatellite markers to examine the genetic structures of Centropomus undecimalis (Bloch, 1792 and Epinephelus marginatus (Lowe, 1834 populations collected from artisanal fishing sites along a stretch of coastline in southeastern Brazil. Based on F-statistics, there was no significant genetic differentiation evident in any C. undecimalis samples (FST=0.012. However, Bayesian clustering, principal component analysis (PCA and discriminant analysis of principal components (DAPC results suggested that there were most likely two clusters, with no relation to geographic areas. The bottleneck results showed no significant values and the effective population sizes (Ne for the two genetically differentiated groups were large and similar. In contrast, for E. marginatus populations, the microsatellite loci showed no population subdivisions. The FST value was low and non-significant (FST=0.008, a Bayesian analysis indicated one cluster, and a PCA showed that all samples from different geographical sites shared the same genetic structure. The bottleneck results exhibited significant differences, and a low Ne was observed. The results of the genetic study of these two species along the southeastern Brazilian coast suggest that the distinct genetic structure of each species should be taken into account as management units for the conservation of their genetic diversities.

  13. Fitting Analysis using Differential evolution Optimization (FADO):. Spectral population synthesis through genetic optimization under self-consistency boundary conditions

    Science.gov (United States)

    Gomes, J. M.; Papaderos, P.

    2017-07-01

    The goal of population spectral synthesis (pss; also referred to as inverse, semi-empirical evolutionary- or fossil record approach) is to decipher from the spectrum of a galaxy the mass, age and metallicity of its constituent stellar populations. This technique, which is the reverse of but complementary to evolutionary synthesis, has been established as fundamental tool in extragalactic research. It has been extensively applied to large spectroscopic data sets, notably the SDSS, leading to important insights into the galaxy assembly history. However, despite significant improvements over the past decade, all current pss codes suffer from two major deficiencies that inhibit us from gaining sharp insights into the star-formation history (SFH) of galaxies and potentially introduce substantial biases in studies of their physical properties (e.g., stellar mass, mass-weighted stellar age and specific star formation rate). These are I) the neglect of nebular emission in spectral fits, consequently; II) the lack of a mechanism that ensures consistency between the best-fitting SFH and the observed nebular emission characteristics of a star-forming (SF) galaxy (e.g., hydrogen Balmer-line luminosities and equivalent widths-EWs, shape of the continuum in the region around the Balmer and Paschen jump). In this article, we present fado (Fitting Analysis using Differential evolution Optimization) - a conceptually novel, publicly available pss tool with the distinctive capability of permitting identification of the SFH that reproduces the observed nebular characteristics of a SF galaxy. This so-far unique self-consistency concept allows us to significantly alleviate degeneracies in current spectral synthesis, thereby opening a new avenue to the exploration of the assembly history of galaxies. The innovative character of fado is further augmented by its mathematical foundation: fado is the first pss code employing genetic differential evolution optimization. This, in conjunction

  14. Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity.

    Science.gov (United States)

    Naidoo, Vanessa L; Mann, Jaclyn K; Noble, Christie; Adland, Emily; Carlson, Jonathan M; Thomas, Jake; Brumme, Chanson J; Thobakgale-Tshabalala, Christina F; Brumme, Zabrina L; Brockman, Mark A; Goulder, Philip J R; Ndung'u, Thumbi

    2017-09-01

    In the large majority of cases, HIV infection is established by a single variant, and understanding the characteristics of successfully transmitted variants is relevant to prevention strategies. Few studies have investigated the viral determinants of mother-to-child transmission. To determine the impact of Gag-protease-driven viral replication capacity on mother-to-child transmission, the replication capacities of 148 recombinant viruses encoding plasma-derived Gag-protease from 53 nontransmitter mothers, 48 transmitter mothers, and 47 infected infants were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. All study participants were infected with HIV-1 subtype C. There was no significant difference in replication capacities between the nontransmitter (n = 53) and transmitter (n = 44) mothers (P = 0.48). Infant-derived Gag-protease NL4-3 recombinant viruses (n = 41) were found to have a significantly lower Gag-protease-driven replication capacity than that of viruses derived from the mothers (P HIV mother-to-child transmission bottleneck favors the transmission of consensus-like viruses with lower viral replication capacities.IMPORTANCE Understanding the characteristics of successfully transmitted HIV variants has important implications for preventative interventions. Little is known about the viral determinants of HIV mother-to-child transmission (MTCT). We addressed the role of viral replication capacity driven by Gag, a major structural protein that is a significant determinant of overall viral replicative ability and an important target of the host immune response, in the MTCT bottleneck. This study advances our understanding of the genetic bottleneck in MTCT by revealing that viruses transmitted to infants have a lower replicative ability as well as a higher similarity to the population consensus (in this case HIV subtype C) than those of their mothers. Furthermore, the observation that "consensus-like" virus sequences correspond to

  15. Total and Differential Leukocyte Counts in Relation to Incidence of Diabetes Mellitus: A Prospective Population-Based Cohort Study

    Science.gov (United States)

    Borné, Yan; Smith, J. Gustav; Nilsson, Peter M.; Melander, Olle; Hedblad, Bo; Engström, Gunnar

    2016-01-01

    Objective High concentrations of leukocytes in blood have been associated with diabetes mellitus. This prospective study aimed to explore whether total and differential leukocyte counts are associated with incidence of diabetes. A missense variant R262W in the SH2B3 (SH2B adaptor protein 3) gene, coding for a protein that negatively regulates hematopoietic cell proliferation, was also studied in relation to incidence of diabetes. Methods and Results Leukocyte count and its subtypes (neutrophils, lymphocytes and mixed cells) were analyzed in 26,667 men and women, 45–73 years old, from the population-based Malmö Diet and Cancer study. Information about the R262W polymorphism (rs3184504) in SH2B3 was genotyped in 24,489 subjects. Incidence of diabetes was studied during a mean follow-up of 14 years. Cox proportional hazards regression was used to examine incidence of diabetes by total and differential leukocyte counts. Mendelian randomization analysis using R262W as an instrumental variable was performed with two-stage least squares regression. A total of 2,946 subjects developed diabetes during the follow-up period. After taking several possible confounders into account, concentrations of total leukocyte count, neutrophils and lymphocytes were all significantly associated with incidence of diabetes. The adjusted hazard ratios (95% confidence interval; quartile 4 vs quartile 1) were 1.37 (1.22–1.53) for total leukocytes, 1.33 (1.19–1.49) for neutrophils and 1.29 (1.15–1.44) for lymphocytes. The R262W polymorphism was strongly associated with leukocytes (0.11x109 cells/l per T allele, p = 1.14 x10-12), lymphocytes (p = 4.3 x10-16), neutrophils (p = 8.0 x10-6) and mixed cells (p = 3.0 x10-6). However, there was no significant association between R262W and fasting glucose, HbA1c or incidence of diabetes. Conclusions Concentrations of total leukocytes, neutrophils and lymphocytes are associated with incidence of diabetes. However, the lack of association with the

  16. Avoiding the problem state bottleneck by strategic use of the environment

    NARCIS (Netherlands)

    Borst, Jelmer P.; Buwalda, Trudy A.; van Rijn, Hedderik; Taatgen, Niels A.

    2013-01-01

    We investigated whether environmental support can be used to circumvent the problem state bottleneck in human multitasking. Previously, it was shown that people can only maintain a single chunk of information in their problem state resource, the central part of working memory. Consequently, when the

  17. Equilibrium at a bottleneck when long-run and short-run scheduling preferences diverge

    NARCIS (Netherlands)

    Peer, S.; Verhoef, E.T.

    2013-01-01

    We consider the use of a Vickrey road bottleneck in the context of repetitive scheduling choices, distinguishing between long-run and short-run scheduling preferences. The preference structure reflects that there is a distinction between the (exogenous) 'long-run preferred arrival time', which would

  18. Effect of force and location of bottleneck for particle moving through ...

    Indian Academy of Sciences (India)

    One of the central assumptions to explain appearance of an anomalous diffusion regime in microporous materials is the cancellation of forces experienced by a moving particle at the bottleneck. In this work, we examine this issue of force cancellation inside a microporous material exploring the diffusion path and ...

  19. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

    DEFF Research Database (Denmark)

    Rebolledo-Jaramillo, Boris; Su, Marcia Shu-Wei; Stoler, Nicholas

    2014-01-01

    The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis...

  20. The nocturnal bottleneck and the evolution of activity patterns in mammals

    NARCIS (Netherlands)

    Gerkema, Menno P.; Davies, Wayne I. L.; Foster, Russell G.; Menaker, Michael; Hut, Roelof A.

    2013-01-01

    In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals

  1. Congestion tolling in the bottleneck model with heterogeneous values of time

    NARCIS (Netherlands)

    van den Berg, V.A.C.; Verhoef, E.T.

    2011-01-01

    When analysing the effects of transport policies it is important to adequately control for heterogeneity: previous studies note that ignoring heterogeneity biases the estimated welfare effects of tolling. This paper examines the effects of tolling, in a bottleneck model, with a continuously

  2. Saccadic Eye Movements Impose a Natural Bottleneck on Visual Short-Term Memory

    Science.gov (United States)

    Ohl, Sven; Rolfs, Martin

    2017-01-01

    Visual short-term memory (VSTM) is a crucial repository of information when events unfold rapidly before our eyes, yet it maintains only a fraction of the sensory information encoded by the visual system. Here, we tested the hypothesis that saccadic eye movements provide a natural bottleneck for the transition of fragile content in sensory memory…

  3. Effect of force and location of bottleneck for particle moving through ...

    Indian Academy of Sciences (India)

    Anirban Sharma

    this work, we examine this issue of force cancellation inside a microporous material exploring the diffusion path and cross-checking bottleneck associated ... viding accurate and specific separation of gases.1,2 They are widely used to separate ... ery to the cancer cells.9,10 Self-diffusion of the drug inside host zeolite is an ...

  4. Two invasive populations of the dry rot fungus Serpula lacrymans show divergent population genetic structures.

    Science.gov (United States)

    Engh, Ingeborg Bjorvand; Carlsen, Tor; Saetre, Glenn-Peter; Högberg, Nils; Doi, Shuichi; Kauserud, Håvard

    2010-02-01

    The dry rot fungus Serpula lacrymans is a devastating basidiomycete occurring in wooden constructions in temperate regions worldwide. In this study, we compare the genetic structures of two invasive populations from Europe and Japan. Microsatellite data from 14 loci and DNA sequences from four loci demonstrated that the two populations were highly differentiated. Significant isolation by distance effect was observed in Europe and Japan. Higher genetic variation was observed within the Japanese population than within the European population, corresponding with the observed higher richness of vegetative compatibility types in Japan, indicating that there has been a higher level of gene flow from the Asian source populations to Japan than to Europe. The European population is genetically more homogenous with only six detected vegetative compatibility types. Various tests indicate that both the European and the Japanese populations have gone through population bottlenecks prior to population expansion. No identical multi-locus genotypes were observed within Japan and very few within Europe, indicating limited clonal dispersal. Deviations from Hardy Weinberg expectations were observed both in Europe and Japan and heterozygote excess were observed at several loci, especially in Europe. Possible explanations for this pattern are discussed.

  5. Allozyme variation in Czech populations of the invasive spiny-cheek crayfish Orconectes limosus (Cambaridae

    Directory of Open Access Journals (Sweden)

    L. Filipová

    2009-01-01

    Full Text Available The North American spiny-cheek crayfish, Orconectes limosus, was most probably introduced into Europe only once, in 1890. The size of the founding population was just 90 individuals. Low genetic variability resulting from a bottleneck effect during introduction might therefore be supposed in European spiny-cheek crayfish populations. On the other hand, the fast spread of O. limosus in Europe and colonisation of various habitats suggest that this species does not suffer from inbreeding depression due to an introduction bottleneck. We analysed 14 O. limosus populations from the Czech Republic using allozyme electrophoresis to evaluate the level of intra- and among-population genetic variation. Out of eight well-scoring allozyme loci chosen for detailed analysis, six were variable in studied populations, suggesting that sufficient variability was maintained during the introduction. Genetic differentiation of Czech populations of the spiny-cheek crayfish was relatively low and did not show any clear geographic pattern, probably due to long-range translocations by humans.

  6. Genetic structure, habitat fragmentation and bottlenecks in Danish bank votes (Clethrionomys glareolus)

    DEFF Research Database (Denmark)

    Redeker, S; Andersen, LW; Pertoldi, C

    2006-01-01

    habitat requirements favouring woodlots, hedgerows and deciduous forests as their prime living area. Hence, a natural or human-induced fragmentation of the forest may cause a sub-structuring of the populations and thereby a restriction of dispersal among populations. The sub-structuring indicated...... by the observed significant genetic differentiation among the five geographically distinct Localities (F-st=0.033, P habitat fragmentation or a combination of home range behaviour and different tree composition in the forests. A road situated between two adjacent forests...

  7. Childhood osteomyelitis-incidence and differentiation from other acute onset musculoskeletal features in a population-based study

    Directory of Open Access Journals (Sweden)

    Reiseter Tor

    2008-10-01

    Full Text Available Abstract Background Osteomyelitis can be difficult to diagnose and there has previously not been a prospective approach to identify all children in a defined geographic area. The aim of this study was to assess the annual incidence of osteomyelitis in children, describe the patient and disease characteristics in those with acute ( Methods In a population-based Norwegian study physicians were asked to refer all children with suspected osteomyelitis. Children with osteomyelitis received follow-up at six weeks, six months and thereafter as long as clinically needed. Results The total annual incidence rate of osteomyelitis was 13 per 100 000 (acute osteomyelitis 8 and subacute osteomyelitis 5 per 100 000. The incidence was higher in patients under the age of 3 than in older children (OR 2.9, 95%: CI 2.3–3.7. The incidence of non-vertebral osteomyelitis was higher than the incidence of vertebral osteomyelitis (10 vs. 3 per 100 000; p = .002. Vertebral osteomyelitis was more frequent in girls than in boys (OR 7.0, 95%: CI 3.3–14.7. ESR ≥ 40 mm/hr had the highest positive predictive laboratory value to identify osteomyelitis patients at 26% and MRI had a positive predictive value of 85%. Long-bone infection was found in 16 (43% patients. ESR, CRP, white blood cell count, neutrophils and platelet count were higher for patients with acute osteomyelitis than for patients with subacute osteomyelitis. Subacute findings on MRI and doctor's delay were more common in subacute osteomyelitis than in acute osteomyelitis patients. Blood culture was positive in 26% of the acute osteomyelitis patients and was negative in all the subacute osteomyelitis patients. Conclusion The annual incidence of osteomyelitis in Norway remains high. ESR values and MRI scan may help to identify osteomyelitis patients and differentiate acute and subacute osteomyelitis.

  8. Unravelling the differential functions and regulation of striatal neuron sub-populations in motor control, reward and motivational processes

    Directory of Open Access Journals (Sweden)

    Sabrina eEna

    2011-07-01

    Full Text Available The striatum, the major input structure of the basal ganglia, is critically involved in motor control and learning of habits and skills, and is also involved in motivational and reward processes. The dorsal striatum, caudate-putamen, is primarily implicated in motor functions whereas the ventral striatum, the nucleus accumbens, is essential for motivation and drug reinforcement. Severe basal ganglia dysfunction occurs in movement disorders as Parkinson’s and Huntington’s disease, and in psychiatric disorders such as schizophrenia and drug addiction. The striatum is essentially composed of GABAergic medium-sized spiny neurons (MSNs that are output neurons giving rise to the so-called direct and indirect pathways and are targets of the cerebral cortex and mesencephalic dopaminergic neurons. Although the involvement of striatal sub-areas in motor control and motivation has been thoroughly characterized, major issues remained concerning the specific and respective functions of the two MSNs sub-populations, D2R-striatopallidal (dopamine D2 receptor-positive and D1R-striatonigral (dopamine D1 receptor-positive neurons, as well as their specific regulation. Here, we review recent advances that gave new insight in the understanding of the differential roles of striatopallidal and striatonigral neurons in the basal ganglia circuit. We discuss innovative techniques developed in the last decade which allowed a much precise evaluation of molecular pathways implicated in motivational processes and functional roles of striatopallidal and striatonigral neurons in motor control and in the establishment of reward-associated behaviour.

  9. Proteomic characterization of mesenchymal stem cell-like populations derived from ovine periodontal ligament, dental pulp, and bone marrow: analysis of differentially expressed proteins.

    Science.gov (United States)

    Mrozik, Krzysztof M; Zilm, Peter S; Bagley, Christopher J; Hack, Sandra; Hoffmann, Peter; Gronthos, Stan; Bartold, P Mark

    2010-10-01

    Postnatal mesenchymal stem/stromal-like cells (MSCs) including periodontal ligament stem cells (PDLSCs), dental pulp stem cells (DPSCs), and bone marrow stromal cells (BMSCs) are capable of self-renewal and differentiation into multiple mesenchymal cell lineages. Despite their similar expression of MSC-associated and osteoblastic markers, MSCs retain the capacity to generate structures resembling the microenvironments from which they are derived in vivo and represent a promising therapy for the regeneration of complex tissues in the clinical setting. With this in mind, systematic approaches are required to identify the differential protein expression patterns responsible for lineage commitment and mediating the formation of these complex structures. This is the first study to compare the differential proteomic expression profiles of ex vivo-expanded ovine PDLSCs, DPSCs, and BMSCs derived from an individual donor. The two-dimensional electrophoresis was performed and regulated proteins were identified by liquid chromatography--electrospray-ionization tandem mass spectrometry (MS and MS/MS), database searching, and de novo sequencing. In total, 58 proteins were differentially expressed between at least 2 MSC populations in both sheep, 12 of which were up-regulated in one MSC population relative to the other two. In addition, the regulation of selected proteins was also conserved between equivalent human MSC populations. We anticipate that differential protein expression profiling will provide a basis for elucidating the protein expression patterns and molecular cues that are crucial in specifying the characteristic growth and developmental capacity of dental and non-dental tissue-derived MSC populations. These expression patterns can serve as important tools for the regeneration of particular tissues in future stem cell-based tissue engineering studies using animal models.

  10. Genetic spatial structure of European common hamsters (Cricetus cricetus) - a result of repeated range expansion and demographic bottlenecks

    NARCIS (Netherlands)

    Neumann, K.; Michaux, R.; Maak, S.; Jansman, H.A.H.; Kayser, A.; Mundt, G.; Gattermann, R.

    2005-01-01

    The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong

  11. Population stochastic modelling (PSM)-An R package for mixed-effects models based on stochastic differential equations

    DEFF Research Database (Denmark)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode

    2009-01-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model......)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornoe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum...... likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODES) with an observation link that incorporates noise. This state-space formulation only...

  12. The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan.

    Directory of Open Access Journals (Sweden)

    Ryosuke Imai

    Full Text Available The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation in gametophytes: mixed (M type and separate (S type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type. Past effective population sizes (Ne were inferred using Approximate Bayesian computation (ABC. The values of fixation index (FIS, allelic richness (AR and gene diversity (h differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152 and the S-type (FIS: 0.208, AR: 2.718, h: 0.367 populations (when admixed individuals were removed from two populations. Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F'ST = 0.739, there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.

  13. The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan.

    Science.gov (United States)

    Imai, Ryosuke; Tsuda, Yoshiaki; Matsumoto, Sadamu; Ebihara, Atsushi; Watano, Yasuyuki

    2016-01-01

    The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern) shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation) in gametophytes: mixed (M) type and separate (S) type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type). Past effective population sizes (Ne) were inferred using Approximate Bayesian computation (ABC). The values of fixation index (FIS), allelic richness (AR) and gene diversity (h) differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152) and the S-type (FIS: 0.208, AR: 2.718, h: 0.367) populations (when admixed individuals were removed from two populations). Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F'ST = 0.739), there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.

  14. Population differentiation of the shore crab Carcinus maenas (Brachyura: Portunidae on the southwest English coast based on genetic and morphometric analyses

    Directory of Open Access Journals (Sweden)

    Inês C. Silva

    2010-08-01

    Full Text Available Carcinus maenas has a planktonic larval phase which can potentially disperse over large distances. Consequently, larval transport is expected to play an important role in promoting gene flow and determining population structure. In the present study, population structuring on the southwest coast of England was analysed using molecular and morphometric approaches. Variation at eight microsatellite loci suggested that the individuals sampled within this region comprise a single genetic population and that gene flow among them is not restricted. Nevertheless, the FST values estimated across loci for all populations suggested that the Tamar population was significantly different from the Exe, Camel and Torridge populations. This differentiation is not explained by isolation by distance, and coastal hydrological events that are apparently influencing larval flux might be the cause of this pattern. Morphometric analysis was also performed. Analysis of carapace and chela shape variation using landmark-based geometric morphometrics revealed extensive morphological variability, as the multivariate analysis of variance showed significant morphometric differences among geographic groups for both sexes. Thus, the morphological differentiation found may be a plastic response to habitat-specific selection pressures.

  15. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations.

    Science.gov (United States)

    Munshi-South, Jason; Zolnik, Christine P; Harris, Stephen E

    2016-04-01

    Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

  16. A genetic association study between growth differentiation factor 5 (GDF 5 polymorphism and knee osteoarthritis in Thai population

    Directory of Open Access Journals (Sweden)

    Sura Thanyachai

    2011-09-01

    Full Text Available Abstract Objective Osteoarthritis (OA is a multi-factorial disease and genetic factor is one of the important etiologic risk factors. Various genetic polymorphisms have been elucidated that they might be associated with OA. Recently, several studies have shown an association between Growth Differentiation Factor 5(GDF5 polymorphism and knee OA. However, the role of genetic predisposing factor in each ethnic group cannot be replicated to all, with conflicting data in the literatures. Therefore, the aim of this study was to investigate the association between GDF5 polymorphism and knee OA in Thai population. Materials and Methods One hundred and ninety three patients aged 54-88 years who attended Ramathibodi Hospital were enrolled. Ninety cases with knee OA according to American College of Rheumatology criteria and one hundred and three cases in control group gave informed consent. Blood sample (5 ml were collected for identification of GDF5 (rs143383 single nucleotide polymorphism by PCR/RFLP according to a standard protocol. This study protocol was approved by the Ethics Committee on human experimentation of Ramathibodi Hospital Faculty of Medicine, Mahidol University. Odds ratios (OR and 95% confidence intervals were calculated for the risk of knee OA by genotype (TT, TC and CC and allele (T/C analyses. Results The baseline characteristics between two groups including job, smoking and activity were not different, except age and BMI. The entire cases and controls were in Hardy-Weinberg equilibrium (p > 0.05. The OA knee group (n = 90 had genotypic figure which has shown by TT 42.2% (n = 38, TC 45.6% (n = 41 and CC 12% (n = 11, whereas the control group (n = 103 revealed TT 32% (n = 33, TC 45.6% (n = 47, and CC 22.3% (n = 23, respectively. Genotypic TT increased risk of knee OA as compared to CC [OR = 2.41 (P = 0.04, 95%CI = 1.02-5.67]. In the allele analysis, the T allele was found to be significantly associated with knee OA [OR = 1.53 (P = 0

  17. Genetic diversity of and differentiation among five populations of blunt snout bream (Megalobrama amblycephala revealed by SRAP markers: implications for conservation and management.

    Directory of Open Access Journals (Sweden)

    Wei Ji

    Full Text Available The blunt snout bream (Megalobrama amblycephala is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian and one genetic strain ('Pujiang No. 1' of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h and Shannon's information index (I values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>'Pujiang No. 1'>Yuni Lake. Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations, Nanxian and 'Pujiang No. 1' (cultured population and genetically selected strain, and Yuni Lake (natural population. Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA, with more genetic divergence existing among populations (55.49%, than within populations (44.51%. This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish.

  18. Discrepancy in the degree of population differentiation between color-morph frequencies and neutral genetic loci in the damselfly Ischnura senegalensis in Okinawa Island, Japan.

    Science.gov (United States)

    Inomata, Nobuyuki; Hironaka, Kumiko; Sawada, Kouji; Kuriwada, Takashi; Yamahira, Kazunori

    2015-06-01

    Evaluation of relative contribution of natural selection and stochastic processes to population differentiation has been of great interest in evolutionary biology. In a damselfly, Ischnura senegalensis, females show color dimorphism (gynochrome vs. androchrome), and color-morph frequencies are known to greatly vary among local populations within Okinawa Island, a small island of Ryukyu Archipelago, Japan. In this study, to examine the effects of natural selection and stochastic processes on the within-island variation in color-morph frequencies, we compared the degree of population differentiation at the color-morph locus with that at a mitochondrial DNA region and ten nuclear microsatellite loci. F ST values at the neutral loci were close to zero, indicating presence of sufficient gene flow (dispersal of adult individuals) between the local populations. In contrast, F ST values at the color-morph locus were significantly different from zero. These results suggest that variation in female color-morph frequencies observed among local populations in Okinawa Island has been caused by divergent selection acting on the phenotype and/or genes tightly linked with the color locus.

  19. Postglacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad-tailed hummingbird (Selasphorus platycercus).

    Science.gov (United States)

    Malpica, Andreia; Ornelas, Juan Francisco

    2014-02-01

    Unlike other migratory hummingbirds in North America, the broad-tailed hummingbird (Selasphorus platycercus) exhibits both long-distance migratory behaviour in the USA and sedentary behaviour in Mexico and Guatemala. We examined the evolution of migration linked to its northward expansion using a multiperspective approach. We analysed variation in morphology, mitochondrial and nuclear DNA, estimated migration rates between migratory and sedentary populations, compared divergence times with the occurrence of Quaternary climate events and constructed species distribution models to predict where migratory and sedentary populations resided during the Last Glacial Maximum (LGM) and Last Interglacial (LIG) events. Our results are consistent with a recent northward population expansion driven by migration from southern sedentary populations. Phylogeographical analyses and population genetics methods revealed that migratory populations in the USA and sedentary populations in Mexico of the platycercus subspecies form one admixed population, and that sedentary populations from southern Mexico and Guatemala (guatemalae) undertook independent evolutionary trajectories. Species distribution modelling revealed that the species is a niche tracker and that the climate conditions associated with modern obligate migrants in the USA were not present during the LIG, which provides indirect evidence for recent migratory behaviour in broad-tailed hummingbirds on the temporal scale of glacial cycles. The finding that platycercus hummingbirds form one genetic population and that suitable habitat for migratory populations was observed in eastern Mexico during the LIG also suggests that the conservation of overwintering sites is crucial for obligate migratory populations currently facing climate change effects. © 2013 John Wiley & Sons Ltd.

  20. Understanding of empty container movement: A study on a bottleneck at an off-dock depot

    Science.gov (United States)

    Zain, Rosmaizura Mohd; Rahman, Mohd Nizam Ab; Nopiah, Zulkifli Mohd; Saibani, Nizaroyani

    2014-09-01

    Port not only function as connections between marine and land transportation but also as core business areas. In a port terminal, available space is limited, but the influx of container is growing. The off-dock depot is one of the key supply chain players that hold empty containers in the inventory. Therefore, this paper aims to identify the main factors of bottlenecks or congestion that hinder the rapid movement of empty containers from the off-dock depot to the customers. Thirty interviews were conducted with individuals who are key players in the container supply chain. The data were analyzed using Atlas.ti software and the analytic hierarchy process to rank the priority factors of bottlenecks. Findings show that several pertinent factors act as barriers to the key players in the container movement in the day-to-day operations. In future studies, strategies to overcome fragmentation in the container supply chain and logistics must be determined.

  1. Squeezing through the Now-or-Never bottleneck: Reconnecting language processing, acquisition, change, and structure.

    Science.gov (United States)

    Chater, Nick; Christiansen, Morten H

    2016-01-01

    If human language must be squeezed through a narrow cognitive bottleneck, what are the implications for language processing, acquisition, change, and structure? In our target article, we suggested that the implications are far-reaching and form the basis of an integrated account of many apparently unconnected aspects of language and language processing, as well as suggesting revision of many existing theoretical accounts. With some exceptions, commentators were generally supportive both of the existence of the bottleneck and its potential implications. Many commentators suggested additional theoretical and linguistic nuances and extensions, links with prior work, and relevant computational and neuroscientific considerations; some argued for related but distinct viewpoints; a few, though, felt traditional perspectives were being abandoned too readily. Our response attempts to build on the many suggestions raised by the commentators and to engage constructively with challenges to our approach.

  2. Population Structure Analysis of Bull Genomes of European and Western Ancestry

    DEFF Research Database (Denmark)

    Chung, Neo Christopher; Szyda, Joanna; Frąszczak, Magdalena

    2017-01-01

    Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources...... and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models...... for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6...

  3. Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life-history traits

    DEFF Research Database (Denmark)

    Hartvig, Ida; So, Thea; Changtragoon, Suchitra

    2018-01-01

    of the distribution area, particularly in Cambodia. We suggest that this pattern is ancient, reflecting the demographic history of the species and possible location of refugia during earlier time periods with limited forest cover, which was supported by signs of old genetic bottlenecks. The D. oliveri populations had...... from populations across Indochina and relates it to landscape characteristics and life-history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center...... generally high levels of genetic diversity (mean He = 0.73), but also strong genetic differentiation among populations (global GST = 0.13), while D. cochinchinensis had a moderate level of genetic diversity (mean He = 0.55), and an even stronger level of differentiation (global GST = 0...

  4. An assessment of The Capacity Drops at The Bottleneck Segments: A review on the existing methodologies

    Directory of Open Access Journals (Sweden)

    Sugiarto Sugiarto

    2015-08-01

    Full Text Available The term of capacity is very useful to quantify the ability of transport facilities in terms of carrying traffic. The capacity of the road is an essential ingredient in the planning, design, and operation of roadways. It is desirable for traffic analyst to be able to predict the time and places where congestion will occur and the volumes to be expected. Most of urbanized areas have been experiencing of traffic congestion problems particularly at urban arterial systems. High traffic demand and limited supply of roadways are always the main factors produced traffic congestion. However, there are other sources of local and temporal congestion, such as uncontrolled access point, median opening and on-street parking activities, which are caused a reduction of roadway capacity during peak operations. Those locations could result in reduction of travel speed and road, as known as hidden bottlenecks. This is bottleneck which is without any changes in geometric of the segments. The Indonesian Highway Capacity Manual (IHCM, 1997 is used to assess urban arterial systems till current days. IHCM provides a static method for examining the capacityand does not systematically take into account of bottleneck activities. However, bottleneck activities create interruption smooth traffic flow along arterial streets, which in turns stimulate related problems, such as, excessive air pollution, additional energy consumption and driver’s frustration due to traffic jammed. This condition could happen simultaneously; mostly repetitive and predictable in same peak hour demands. Therefore, this paper carefully summarize on the existing methodologies considering required data, handled data processing and expected output of each proposed of analysis. We further notice that dynamic approach could be more appropriated for analyzing temporal congestion segments (median opening, on street parking, etc.. Method of oblique cumulative plot seems to be more applicable in terms of

  5. Population Differentiation and Hybridisation of Australian Snubfin (Orcaella heinsohni) and Indo-Pacific Humpback (Sousa chinensis) Dolphins in North-Western Australia

    Science.gov (United States)

    Brown, Alexander M.; Kopps, Anna M.; Allen, Simon J.; Bejder, Lars; Littleford-Colquhoun, Bethan; Parra, Guido J.; Cagnazzi, Daniele; Thiele, Deborah; Palmer, Carol; Frère, Celine H.

    2014-01-01

    Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins (‘snubfin’ and ‘humpback dolphins’, hereafter) of north-western Australia. While both species are listed as ‘near threatened’ by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (FST = 0.05–0.09; Pgenetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin. PMID:24988113

  6. GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

    Directory of Open Access Journals (Sweden)

    Sudarto Sudarto

    2008-12-01

    Full Text Available Research on genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra, based on sequencing gene of mtDNA Cytochrome b and nucleus DNA RAG2 has been done. The objectives of the study were to obtain the representation of genetic differentiation among population of clown loach fishes or botia (Chromobotia macracanthus from Sumatra and Kalimantan and to estimate the time divergence of both population group of botia. Samples of botia population were taken from 3 rivers in Sumatra namely Batanghari, Musi, and Tulang Bawang and one river from Kalimantan namely Kapuas. The genetic analysis was based on the sequencing of mtDNA Cytochrome b and nucleus DNA RAG2. The statistical analysis was done by using APE package on R language. The parameters observed were: nucleotide diversity, genetic distance, and neighbor-joining tree. The result showed that the highest nucleotide diversity was fish population of Musi, while the other two populations, Tulang Bawang (Sumatra and Kapuas (Kalimantan, were considered as the lowest genetic diversity especially based on nucleus DNA RAG2 sequencing. Based on mtDNA Cytochrome-b sequencing, the most distinct population among those populations based on genetic distance were fish populations of Musi and Kapuas. According to the result of neighbor-joining tree analysis, the populations of botia were classified into two groups namely group of Sumatra and group of Kalimantan. The estimation of time divergence among group of population of Sumatra and Kalimantan based on mtDNA Cytochrome b was about 9.25—9.46 million years (Miocene era. The high genetic differences between groups of Sumatra and Kalimantan suggested that the effort of restocking botia from Sumatra into Kalimantan has to be done carefully, because it may disturb the gene originality of both botia populations.

  7. Evaluation of average travel delay caused by moving bottlenecks on highways.

    Science.gov (United States)

    Wei, Xueyan; Xu, Chengcheng; Wang, Wei; Yang, Menglin; Ren, Xiaoma

    2017-01-01

    This paper presents a modelling framework to evaluate travel delay of all vehicles influenced by moving bottlenecks on highways. During the derivation of analytical formulas, the arrival of slow vehicles was approximated by a Poisson process based on the assumption that they occupied a constant low proportion of the traffic stream. The mathematical analysis process was developed from moving bottlenecks with the same velocity to those with multiple different velocities, and the closed-form expression of expected average travel delay was obtained by utilizing kinematic-wave moving bottleneck theory, gap acceptance theory, probability theory and renewal theory. Model validation and parameters sensitive analysis were conducted by simulation relying on the open source database of US highway 10. The maximum passing rate and the macroscopic parameters of initial traffic state with maximum delay could be found by means of approximate formulas. The proposed modeling framework can be applied for evaluating impacts of slow vehicles on highway operation quantifiably, based on which traffic managements like truck prohibited period decision and speed or lane restriction could be made more scientifically.

  8. Managing bottlenecks in manual automobile assembly systems using discrete event simulation

    Directory of Open Access Journals (Sweden)

    Dewa, M.

    2013-08-01

    Full Text Available Batch model lines are quite handy when the demand for each product is moderate. However, they are characterised by high work-in-progress inventories, lost production time when changing over models, and reduced flexibility when it comes to altering production rates as product demand changes. On the other hand, mixed model lines can offer reduced work-in-progress inventory and increased flexibility. The object of this paper is to illustrate that a manual automobile assembling system can be optimised through managing bottlenecks by ensuring high workstation utilisation, reducing queue lengths before stations and reducing station downtime. A case study from the automobile industry is used for data collection. A model is developed through the use of simulation software. The model is then verified and validated before a detailed bottleneck analysis is conducted. An operational strategy is then proposed for optimal bottleneck management. Although the paper focuses on improving automobile assembly systems in batch mode, the methodology can also be applied in single model manual and automated production lines.

  9. Origin of the correlations between exit times in pedestrian flows through a bottleneck

    Science.gov (United States)

    Nicolas, Alexandre; Touloupas, Ioannis

    2018-01-01

    Robust statistical features have emerged from the microscopic analysis of dense pedestrian flows through a bottleneck, notably with respect to the time gaps between successive passages. We pinpoint the mechanisms at the origin of these features thanks to simple models that we develop and analyse quantitatively. We disprove the idea that anticorrelations between successive time gaps (i.e. an alternation between shorter ones and longer ones) are a hallmark of a zipper-like intercalation of pedestrian lines and show that they simply result from the possibility that pedestrians from distinct ‘lines’ or directions cross the bottleneck within a short time interval. A second feature concerns the bursts of escapes, i.e. egresses that come in fast succession. Despite the ubiquity of exponential distributions of burst sizes, entailed by a Poisson process, we argue that anomalous (power-law) statistics arise if the bottleneck is nearly congested, albeit only in a tiny portion of parameter space. The generality of the proposed mechanisms implies that similar statistical features should also be observed for other types of particulate flows.

  10. TASEP on parallel tracks: Effects of mobile bottlenecks in fixed segments

    Science.gov (United States)

    Sinha, Sumit; Chowdhury, Debashish

    2015-07-01

    We study the flux of totally asymmetric simple exclusion processes (TASEPs) on a twin co-axial square tracks. In this biologically motivated model the particles in each track act as mobile bottlenecks against the movement of the particles in the other although the particles are not allowed to move out of their respective tracks. So far as the outer track is concerned, the particles on the inner track act as bottlenecks only over a set of fixed segments of the outer track, in contrast to site-associated and particle-associated quenched randomness in the earlier models of disordered TASEP. In a special limiting situation the movement of particles in the outer track mimic a TASEP with a "point-like" immobile (i.e., quenched) defect where phase segregation of the particles is known to take place. The length of the inner track as well as the strength and number density of the mobile bottlenecks moving on it are the control parameters that determine the nature of spatio-temporal organization of particles on the outer track. Variation of these control parameters allows variation of the width of the phase-coexistence region on the flux-density plane of the outer track. Some of these phenomena are likely to survive even in the future extensions intended for studying traffic-like collective phenomena of polymerase motors on double-stranded DNA.

  11. The nocturnal bottleneck and the evolution of activity patterns in mammals.

    Science.gov (United States)

    Gerkema, Menno P; Davies, Wayne I L; Foster, Russell G; Menaker, Michael; Hut, Roelof A

    2013-08-22

    In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.

  12. Supply chain bottlenecks in the South African construction industry: Qualitative insights

    Directory of Open Access Journals (Sweden)

    Poobalan Pillay

    2017-01-01

    Full Text Available Background: The construction industry in South Africa has a lot of potential but its performance is still restricted by numerous internal and external challenges. Unless these challenges are identified and understood better, further growth of this industry is likely to be hindered, which has negative economic implications for the South African economy.Objectives: This study investigated supply chain bottlenecks faced by the construction industry in South Africa. It also discussed solutions for addressing the identified bottlenecks in order to facilitate the continued development of supply chain management in the construction industry.Method: The study used a qualitative approach in which in-depth interviews were held with purposively selected senior managers drawn from the construction industry in South Africa. Content analysis using ATLAS.ti software was employed to identify the themes from the collected data.Findings: The findings of the study showed that supply chain management in the construction industry in South Africa is constrained by five major bottlenecks: skills and qualifications, procurement practices and systems, supply chain integration, supply chain relationships and the structure of the construction industry. Recommendations for addressing each of these five challenges were put forward.Conclusion: The study concludes that both awareness and application of supply chain management in the construction industry in South Africa remains inhibited, which creates opportunities for further improvements in this area to realise the full potential of the industry.

  13. Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest.

    Science.gov (United States)

    Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

    2007-11-01

    Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals.

  14. [Differentiation of the mitochondrial subhaplogroup U4 in the populations of Eastern Europe, Ural, and Western Siberia: implication to the genetic history of the Uralic populations].

    Science.gov (United States)

    Maliarchuk, B A

    2004-11-01

    Phylogenetic relationships between the sequences of the mitochondrial DNA (mtDNA) hypervariable segment 1, belonging to subhaplogroup U4, were examined in the populations of Eastern Europe, Ural, and Northwest Siberia. It was shown that the frequency of subhaplogroup U4, as well as its proportion in the U-component of the gene pools, increased eastwards, reaching maximum values in the populations of Northwest Siberia. Phylogenetic analysis it was showed that the appearance of specific U4-lineage (16113C-16356-16362) in the ancestors of Mansi was most likely caused by its divergence from the East European cluster 16356-16362 in the Late Upper Paleolithic (18566 +/- 12915 years before present). Other U4 mtDNA lineages (16189-16356 and 16311-16356), typical mostly of the indigenous populations of Northwest Siberia (Mansi, Nganasans, and Kets) may have formed during the Neolithic-early Bronze Age (6055 +/- 3599 years before present, on average). It seems likely that the isolation of ancient populations inhabiting the region between the Ob' and Yenisei rivers was the key factor, providing the appearance of the unique Caucasoid mtDNA lineages in their gene pools. These results were consistent with the traditional point of view on the mixed origin of the Finno-Ugric populations of the Volga-Ural region and West Siberia, resulted from the genetic relationships between the populations of Europe and Asia.

  15. Ecological comparison of cellular stress responses among populations - normalizing RT-qPCR values to investigate differential environmental adaptations

    National Research Council Canada - National Science Library

    Koenigstein, Stefan; Pöhlmann, Kevin; Held, Christoph; Abele, Doris

    2013-01-01

    Rising temperatures and other environmental factors influenced by global climate change can cause increased physiological stress for many species and lead to range shifts or regional population extinctions...

  16. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

    Science.gov (United States)

    Cai, Xiaoyun; Qin, Zhendong; Wen, Bo; Xu, Shuhua; Wang, Yi; Lu, Yan; Wei, Lanhai; Wang, Chuanchao; Li, Shilin; Huang, Xingqiu; Jin, Li; Li, Hui

    2011-01-01

    Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape), with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia.

  17. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Cai

    Full Text Available Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK and Hmong-Mien (HM speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape, with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia.

  18. BOTTLENECK ANALYSIS AND STRATEGIC PLANNING ON CHILDHOOD DIARRHEA MANAGEMENT IN 6 HIGH PRIORITY DISTRICTS OF GUJARAT

    Directory of Open Access Journals (Sweden)

    Rupani Mihir

    2015-01-01

    Full Text Available Introduction:Bottleneck Analysis and Strategic Planning exercise was carried out in 6 High Priority Districts (HPDs, under Call-to-Action for RMNCH+A strategy.Rationale: In spite of continued efforts, India is still lagging behind in its MDG goals.Objectives: To identify gaps in childhood diarrhea management and propose strategic options for the same.Materials and Methods: Bottleneck analysis exercisewas carried out based on the Tanahashi model, desk review and focused group discussions between district officials, front-line workers and UNICEF officials. These bottlenecks were pertaining to the availability, accessibility, utilization of services and quality of services being provided by the health department.Elaborating the Tanahashi model for the 6 HPDs, 94% of the front-line workers (FLWs had stock of Zinc-ORS; 88% FLWs were trained in diarrhea management; 98% villages had at least one FLW trained in diarrhea management; health care seeking for diarrhea cases was 17%; 5.1% diarrhea cases received Zinc-ORS from health worker and 2.4% care takers prepared Zinc-ORS in safe drinking water.Results: The major bottlenecks identified for Childhood Diarrhea management in the 6 High Priority Districts were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution of Zinc-ORS till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop IEC/BCC plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary latrines

  19. Identification of a unique hepatocellular carcinoma line, Li-7, with CD13(+) cancer stem cells hierarchy and population change upon its differentiation during culture and effects of sorafenib.

    Science.gov (United States)

    Yamada, Takeshi; Abei, Masato; Danjoh, Inaho; Shirota, Ryoko; Yamashita, Taro; Hyodo, Ichinosuke; Nakamura, Yukio

    2015-04-11

    Cancer stem cell (CSC) research has highlighted the necessity of developing drugs targeting CSCs. We investigated a hepatocellular carcinoma (HCC) cell line that not only has CSC hierarchy but also shows phenotypic changes (population changes) upon differentiation of CSC during culture and can be used for screening drugs targeting CSC. Based on a hypothesis that the CSC proportion should decrease upon its differentiation into progenitors (population change), we tested HCC cell lines (HuH-7, Li-7, PLC/PRF/5, HLF, HLE) before and after 2 months culture for several markers (CD13, EpCAM, CD133, CD44, CD90, CD24, CD166). Tumorigenicity was tested using nude mice. To evaluate the CSC hierarchy, we investigated reconstructivity, proliferation, ALDH activity, spheroid formation, chemosensitivity and microarray analysis of the cell populations sorted by FACS. Only Li-7 cells showed a population change during culture: the proportion of CD13 positive cells decreased, while that of CD166 positive cells increased. The high tumorigenicity of the Li-7 was lost after the population change. CD13(+)/CD166(-) cells showed slow growth and reconstructed the bulk Li-7 populations composed of CD13(+)/CD166(-), CD13(-)/CD166(-) and CD13(-)/CD166(+) fractions, whereas CD13(-)/CD166(+) cells showed rapid growth but could not reproduce any other population. CD13(+)/CD166(-) cells showed high ALDH activity, spheroid forming ability and resistance to 5-fluorouracil. Microarray analysis demonstrated higher expression of stemness-related genes in CD166(-) than CD166(+) fraction. These results indicated a hierarchy in Li-7 cells, in which CD13(+)/CD166(-) and CD13(-)/CD166(+) cells serve as slow growing CSCs and rapid growing progenitors, respectively. Sorafenib selectively targeted the CD166(-) fraction, including CD13(+) CSCs, which exhibited higher mRNA expression for FGF3 and FGF4, candidate biomarkers for sorafenib. 5-fluorouracil followed by sorafenib inhibited the growth of bulk Li-7

  20. The genetic structure of a relict population of wood frogs

    Science.gov (United States)

    Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

    2012-01-01

    Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

  1. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-01-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (FST = 0.01) and mitochondrial (ΦST = 0.47; FST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species’ range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  2. Asymbiotic germination response to photoperiod and nutritional media in six populations of Calopogon tuberosus var. tuberosus (Orchidaceae): evidence for ecotypic differentiation.

    Science.gov (United States)

    Kauth, Philip J; Kane, Michael E; Vendrame, Wagner A; Reinhardt-Adams, Carrie

    2008-11-01

    Ecotypic differentiation has been explored in numerous plant species, but has been largely ignored in the Orchidaceae. Applying a specific germination protocol for widespread seed sources may be unreliable due to inherent physiological or genetic differences in localized populations. It is crucial to determine whether ecotypic differentiation exists for restoration and conservation programmes. Calopogon tuberosus var. tuberosus, a widespread terrestrial orchid of eastern North America, is a model species to explore ecotypic differences in germination requirements, as this species occupies diverse habitats spanning a wide geographical range. Mature seeds were collected from south Florida, north central Florida, three locations in South Carolina, and the upper Michigan peninsula. Effects of three photoperiods (8/16, 12/12, 16/8 h L/D) were examined on asymbiotic in vitro seed germination and seedling development of C. tuberosus. Germination and early development was monitored for 8 weeks, while advanced development was monitored for an additional 8 weeks. In an additional experiment, asymbiotic seed germination and development was monitored for 8 weeks on six culture media (BM-1 terrestrial orchid medium, Knudson C, Malmgrem, half-strength MS, P723, and Vacin and Went). A tetrazolium test for embryo viability was performed. Short days promoted the highest germination among Florida populations, but few differences among photoperiods in other seed sources existed. Different media had little effect on the germination of Michigan and Florida populations, but germination of South Carolina seeds was higher on media with higher calcium and magnesium. Tetrazolium testing confirmed that South Carolina seeds exhibited low viability while viability was higher in Florida seeds. Seed germination and corm formation was rapid in Michigan seeds across all treatments. Michigan seedlings allocated more biomass to corms compared with other seed sources. Rapid germination and corm

  3. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.

  4. Asymbiotic Germination Response to Photoperiod and Nutritional Media in Six Populations of Calopogon tuberosus var. tuberosus (Orchidaceae): Evidence for Ecotypic Differentiation

    Science.gov (United States)

    Kauth, Philip J.; Kane, Michael E.; Vendrame, Wagner A.; Reinhardt-Adams, Carrie

    2008-01-01

    Background and Aims Ecotypic differentiation has been explored in numerous plant species, but has been largely ignored in the Orchidaceae. Applying a specific germination protocol for widespread seed sources may be unreliable due to inherent physiological or genetic differences in localized populations. It is crucial to determine whether ecotypic differentiation exists for restoration and conservation programmes. Calopogon tuberosus var. tuberosus, a widespread terrestrial orchid of eastern North America, is a model species to explore ecotypic differences in germination requirements, as this species occupies diverse habitats spanning a wide geographical range. Methods Mature seeds were collected from south Florida, north central Florida, three locations in South Carolina, and the upper Michigan peninsula. Effects of three photoperiods (8/16, 12/12, 16/8 h L/D) were examined on asymbiotic in vitro seed germination and seedling development of C. tuberosus. Germination and early development was monitored for 8 weeks, while advanced development was monitored for an additional 8 weeks. In an additional experiment, asymbiotic seed germination and development was monitored for 8 weeks on six culture media (BM-1 terrestrial orchid medium, Knudson C, Malmgrem, half-strength MS, P723, and Vacin and Went). A tetrazolium test for embryo viability was performed. Key Results Short days promoted the highest germination among Florida populations, but few differences among photoperiods in other seed sources existed. Different media had little effect on the germination of Michigan and Florida populations, but germination of South Carolina seeds was higher on media with higher calcium and magnesium. Tetrazolium testing confirmed that South Carolina seeds exhibited low viability while viability was higher in Florida seeds. Seed germination and corm formation was rapid in Michigan seeds across all treatments. Michigan seedlings allocated more biomass to corms compared with other seed

  5. A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations.

    Science.gov (United States)

    Campbell, Lewis J; Hammond, S Austin; Price, Stephen J; Sharma, Manmohan D; Garner, Trenton W J; Birol, Inanc; Helbing, Caren C; Wilfert, Lena; Griffiths, Amber G F

    2018-02-08

    Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in non-laboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception amongst others. A large proportion of potential non-coding RNA transcripts present in our differentially expressed set provides first evidence of a possible role for long non-coding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from postitive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  6. Use of Multicolor Flow Cytometry for Isolation of Specific Cell Populations Deriving from Differentiated Human Embryonic Stem Cells

    NARCIS (Netherlands)

    Mengarelli, Isabella; Fryga, Andrew; Barberi, Tiziano

    2016-01-01

    Flow Cytometry-Sorting (FCM-Sorting) is a technique commonly used to identify and isolate specific types of cells from a heterogeneous population of live cells. Here we describe a multicolor flow cytometry technique that uses five distinct cell surface antigens to isolate four live populations with

  7. Strong genetic differentiation among east Atlantic populations of the sword razor shell ( Ensis siliqua) assessed with mtDNA and RAPD markers

    Science.gov (United States)

    Arias, Alberto; Fernández-Moreno, Mercedes; Fernández-Tajes, Juan; Gaspar, Miguel B.; Méndez, Josefina

    2011-03-01

    The sword razor shell Ensis siliqua (Linnaeus, 1758) is a bivalve with a high commercial value being appreciated in fresh and processed markets. However, the genetic studies carried out in populations of E. siliqua are scarce. In this work, the genetic variability and differentiation of the sword razor shell was assessed using PCR-RFLPs of a fragment of the 16S rRNA mitochondrial gene and random amplified polymorphic loci (RAPD) in nine localities from Ireland, Spain, and Portugal. In the 314 individuals examined for the mitochondrial fragment, 12 composite haplotypes were observed; meanwhile, a unique phenotype was observed for each of the 242 individuals analyzed with 61 RAPD loci. Two of the mitochondrial composite haplotypes accounted for the majority of individuals (89.81%) and showed a remarkably disjoint distribution between Irish and Iberian samples, with the exception of Aveiro which exhibited as the most frequent haplotype the same found in Ireland. The level of variability observed for each sample was generally correlated with both types of markers and the results obtained suggest the existence of a strong population differentiation between Irish and Iberian localities, except for the Portuguese sample from Aveiro which is surprisingly closer to Irish individuals, although it is probably highly differentiated.

  8. The impact of share wave elastography in differentiation of hepatic hemangioma from malignant liver tumors in pediatric population.

    Science.gov (United States)

    Özmen, Evrim; Adaletli, Ibrahim; Kayadibi, Yasemin; Emre, Şenol; Kiliç, Fahrettin; Dervişoğlu, Sergülen; Kuruğoğlu, Sebuh; Şenyüz, Osman Faruk

    2014-09-01

    In children it is crucial to differentiate malignant liver tumors from the most common benign tumor, hepatic hemangiomas since the treatment strategies are quite different. We aimed to evaluate the efficiency of shear wave elastography (SWE) technique in differentiation of malignant hepatic tumors and hepatic hemangiomas. Twenty patients with hepatic tumor were included in our study. Two radiologists performed SWE for 13 patients with malignant hepatic tumors including hepatoblastoma (n=7), hepatocellular carcinoma (n=3), metastasis (n=2), embryonal sarcoma (n=1) and 7 patients with hepatic hemangioma. All of our patients were between the age of 1 and 192 months (mean age: 56.88 months). Receiver operating characteristic analysis was achieved to evaluate the diagnostic accuracy of SWE and to determine the optimal cut-off value in differentiation hepatic hemangioma from malignant hepatic tumors. The mean SWE values (in kPa) for the first observer were 46.94 (13.8-145) and 22.38 (6.6-49.6) and those for the second observer were 57.91 (11-237) and 23.87 (6.4-57.5), respectively for malignant hepatic tumors and hepatic hemangiomas. The SWE values of malignant hepatic tumors were significantly higher than those of hepatic hemangioma (p=0.02). The inter-observer agreement was almost perfect (0.81). The area under the receiver operating characteristic curve of SWE for differentiating the hepatic hemangioma from malignant hepatic tumors was 0.77 with a sensitivity of 72.7% and a specificity of 66.7% at a cutoff value of 23.62 with 95% confidence interval. Shear wave elastography can be helpful in differentiation of malignant hepatic tumors and hepatic hemangioma. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  9. Microsatellite-based genetic variability and differentiation of hatchery and feral common carp Cyprinus carpio L. (Cyprinidae, Cypriniformes populations in Croatia

    Directory of Open Access Journals (Sweden)

    Tomljanović Tea

    2013-01-01

    Full Text Available Common carp production has an important status in Croatian aquaculture. In addition, the sport fishing of common carp in open waters is very popular, but it is often based on stocking from fish farms. Using fifteen microsatellites, 243 individuals from 5 hatchery and 5 feral populations have been analyzed. A total number of 148 alleles were recorded. However, the mean number of alleles per locus was remarkably low. Pairwise FST values (0.026-0.130 were significant (P<0.01, demonstrating differentiation among populations. The Markov chain method test showed that all the populations deviated from HWE (P <0.05. After sequential Bonferroni correction only the Vrana lake was in HWE in all the loci but MFW20. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity are discussed. AMOVA results for 10 populations indicate that the percentage of the variation among populations was 6.26%, which is lower than the variation within populations (91.04%.

  10. An efficient experimental strategy for mouse embryonic stem cell differentiation and separation of a cytokeratin-19-positive population of insulin-producing cells.

    Science.gov (United States)

    Naujok, O; Francini, F; Jörns, A; Lenzen, S

    2008-08-01

    Embryonic stem cells are a potential source for insulin-producing cells, but existing differentiation protocols are of limited efficiency. Here, the aim has been to develop a new one, which drives development of embryonic stem cells towards insulin-producing cells rather than to neuronal cell types, and to combine this with a strategy for their separation from insulin-negative cells. The cytokeratin-19 (CK19) promoter was used to control the expression of enhanced yellow fluorescence protein in mouse embryonic stem cells during their differentiation towards insulin-producing cells, using a new optimized four-stage protocol. Two cell populations, CK19(+) and CK19(-) cells, were successfully fluorescence sorted and analysed. The new method reduced neuronal progeny and suppressed differentiation into glucagon- and somatostatin-producing cells. Concomitantly, beta-cell like characteristics of insulin-producing cells were strengthened, as documented by high gene expression of the Glut2 glucose transporter and the transcription factor Pdx1. This novel protocol was combined with a cell-sorting technique. Through the combined procedure, a fraction of glucose-responsive insulin-secreting CK19(+) cells was obtained with 40-fold higher insulin gene expression and 50-fold higher insulin content than CK19(-) cells. CK19(+) cells were immunoreactive for C-peptide and had ultrastructural characteristics of an insulin-secretory cell. Differentiated CK19(+) cells reflect an endocrine precursor cell type of ductal origin, potentially suitable for insulin replacement therapy in diabetes.

  11. [Genetic variability and differentiation of three Russian populations of yellow potato cyst nematode Globodera rostochiensis as revealed by nuclear markers].

    Science.gov (United States)

    Khrisanfova, G G; Kharchevnikov, D A; Popov, I O; Zinov'eva, S V; Semenova, S K

    2008-05-01

    Genetic variability of yellow potato cyst nematode G. rostochiensis from three Russian populations (Karelia, Vladimir oblast, and Moscow oblast) was investigated using two types of nuclear markers. Using RAPD markers identified with the help of six random primers (P-29, OPA-10, OPT-14, OPA-11, OPB-11, and OPH-20), it was possible to distinguish Karelian population from the group consisting of the populations from two adjacent regions (Moscow oblast and Vladimir oblast). Based on the combined matrix, containing 294 RAPD fragments, dendrogram of genetic differences was constructed, and the indices of genetic divergence and partition (P, H, and G(st)), as well as the gene flow indices N(m) between the nematode samples examined, were calculated. The dendrogram structure, genetic diversity indices, and variations of genetic distances between single individuals in each population from Karelia and Central Russia pointed to genetic isolation and higher genetic diversity of the nematodes from Karelia. Based on polymorphism of rDNA first intergenic spacer ITS1, attribution of all populations examined to the species G. rostochiensis was proved. Small variations of the ITS1 sequence in different geographic populations of nematodes from different regions of the species world range did not allow isolation of separate groups within the species. Possible factors (including interregional transportations of seed potato) affecting nematode population structure in Russia are discussed.

  12. Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation.

    Science.gov (United States)

    Leite, K C E; Seixas, G H F; Berkunsky, I; Collevatti, R G; Caparroz, R

    2008-09-09

    The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit.

  13. Postenrichment Population Differentials Using Buffered Listeria Enrichment Broth: Implications of the Presence of Listeria innocua on Listeria monocytogenes in Food Test Samples†

    Science.gov (United States)

    KEYS, ASHLEY L.; DAILEY, RACHEL C.; HITCHINS, ANTHONY D.; SMILEY, R. DERIKE

    2016-01-01

    The recovery of low levels of Listeria monocytogenes from foods is complicated by the presence of competing microorganisms. Nonpathogenic species of Listeria pose a particular problem because variation in growth rate during the enrichment step can produce more colonies of these nontarget cells on selective and/or differential media, resulting in a preferential recovery of nonpathogens, especially Listeria innocua. To gauge the extent of this statistical barrier to pathogen recovery, 10 isolates each of L. monocytogenes and L. innocua were propagated together from approximately equal initial levels using the current U.S. Food and Drug Administration’s enrichment procedure. In the 100 isolate pairs, an average 1.3-log decrease was found in the 48-h enrichment L. monocytogenes population when L. innocua was present. In 98 of the 100 isolate pairs, L. innocua reached higher levels at 48 h than did L. monocytogenes, with a difference of 0.2 to 2.4 log CFU/ml. The significance of these population differences was apparent by an increase in the difficulty of isolating L. monocytogenes by the streak plating method. L. monocytogenes went completely undetected in 18 of 30 enrichment cultures even after colony isolation was attempted on Oxoid chromogenic Listeria agar. This finding suggests that although both Listeria species were present on the plate, the population differential between them restricted L. monocytogenes to areas of the plate with confluent growth and that isolated individual colonies were only L. innocua. PMID:24215687

  14. Postenrichment population differentials using buffered Listeria enrichment broth: implications of the presence of Listeria innocua on Listeria monocytogenes in food test samples.

    Science.gov (United States)

    Keys, Ashley L; Dailey, Rachel C; Hitchins, Anthony D; Smiley, R Derike

    2013-11-01

    The recovery of low levels of Listeria monocytogenes from foods is complicated by the presence of competing microorganisms. Nonpathogenic species of Listeria pose a particular problem because variation in growth rate during the enrichment step can produce more colonies of these nontarget cells on selective and/or differential media, resulting in a preferential recovery of nonpathogens, especially Listeria innocua. To gauge the extent of this statistical barrier to pathogen recovery, 10 isolates each of L. monocytogenes and L. innocua were propagated together from approximately equal initial levels using the current U. S. Food and Drug Administration's enrichment procedure. In the 100 isolate pairs, an average 1.3-log decrease was found in the 48-h enrichment L. monocytogenes population when L. innocua was present. In 98 of the 100 isolate pairs, L. innocua reached higher levels at 48 h than did L. monocytogenes, with a difference of 0.2 to 2.4 log CFU/ml. The significance of these population differences was apparent by an increase in the difficulty of isolating L. monocytogenes by the streak plating method. L. monocytogenes went completely undetected in 18 of 30 enrichment cultures even after colony isolation was attempted on Oxoid chromogenic Listeria agar. This finding suggests that although both Listeria species were present on the plate, the population differential between them restricted L. monocytogenes to areas of the plate with confluent growth and that isolated individual colonies were only L. innocua.

  15. Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean Sea.

    Science.gov (United States)

    De Innocentiis, S; Sola, L; Cataudella, S; Bentzen, P

    2001-09-01

    The dusky grouper, Epinephelus marginatus, inhabits coastal reefs in the Mediterranean Sea and Atlantic Ocean. A decline in the abundance of this long-lived protogynous hermaphrodite has led to its listing as an endangered species in the Mediterranean, and heightened management concerns regarding its genetic variability and population substructure. To address these concerns, we analysed genetic variation at seven microsatellite and 28 allozyme loci in dusky groupers sampled from seven areas (for microsatellites) and three areas (for allozymes) in the west-central Mediterranean. Levels of genetic variability were higher for microsatellites than for allozymes (mean H(E) = 0.78 and 0.07, respectively), but similar to those observed in other marine fishes with comparable markers. Both microsatellites and allozymes revealed significant genetic differentiation among all areas analysed with each class of marker, but the magnitude of differentiation revealed by allozymes over three locales (F(ST) = 0.214) was greater than that detected with microsatellites over seven areas, or over the three areas shared with the allozyme analysis (F(ST) = 0.018 and approximately 0, respectively). A large proportion of the allozyme differentiation was due to a single locus (ADA*) possibly influenced by selection, but allozyme differentiation over the three areas was still highly significant (F(ST) = 0.06, P < 0.0001), and the 95% confidence intervals for allozyme and microsatellite F(ST) did not overlap when this locus was excluded. There was no evidence of isolation by distance with either class of markers. Our results lead us to conclude that dusky groupers are not panmictic in the Mediterranean Sea and suggest that they should be managed on a local basis. However, more work is needed to elucidate genetic relationships among populations.