Significant genetic differentiation within the population of the Island of Corsica (France) revealed by y-chromosome analysis.

Science.gov (United States)

Ghiani, Maria Elena; Varesi, Laurent; Mitchell, Robert John; Vona, Giuseppe

2009-12-01

Using 10 Y-chromosome short tandem repeat allelic and haplotypic frequencies, we examined genetic variation within the population of Corsica and its relationship with other Mediterranean populations. The most significant finding is the high level of genetic differentiation within Corsica, with strong evidence of an effective barrier to male-mediated gene flow between the south and the rest of the island. This internal differentiation most probably results from low exogamy among small isolated populations and also from the orography of the island, with a central mountain chain running the length of the island restricting human movement. This physical barrier is reflected not only in present-day intraisland linguistic and genetic differences but also in the relatedness of Corsican regions to other Mediterranean groups. Northwest and Central Corsica are much closer to West Mediterranean populations, whereas South Corsica is closer to Central-North Sardinia and East Mediterranean populations.

Graphene nanomesh-based devices exhibiting a strong negative differential conductance effect

International Nuclear Information System (INIS)

Hung Nguyen, V; Mazzamuto, F; Saint-Martin, J; Bournel, A; Dollfus, P

2012-01-01

Using atomistic quantum simulation based on a tight binding model, we have investigated the transport characteristics of graphene nanomesh-based devices and evaluated the possibilities of observing negative differential conductance. It is shown that by taking advantage of bandgap opening in the graphene nanomesh lattice, a strong negative differential conductance effect can be achieved at room temperature in pn junctions and n-doped structures. Remarkably, the effect is improved very significantly (with a peak-to-valley current ratio of a few hundred) and appears to be weakly sensitive to the transition length in graphene nanomesh pn hetero-junctions when inserting a pristine (gapless) graphene section in the transition region between n and p zones. The study therefore suggests new design strategies for graphene electronic devices which may offer strong advantages in terms of performance and processing over the devices studied previously. (paper)

Evolutionary dynamics of fluctuating populations with strong mutualism

Science.gov (United States)

Chotibut, Thiparat; Nelson, David

2013-03-01

Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with independent fluctuations in the numbers of two distinct species, in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.

Genetic differentiation between sympatric and allopatric wintering populations of Snow Geese

Science.gov (United States)

Humphries, E.M.; Peters, J.L.; Jonsson, J.E.; Stone, R.; Afton, A.D.; Omland, K.E.

2009-01-01

Blackwater National Wildlife Refuge on the Delmarva Peninsula, Maryland, USA has been the wintering area of a small population of Lesser Snow Geese (Chen caerulescens caerulescens; LSGO) since the 1930s. Snow Geese primarily pair in wintering areas and gene flow could be restricted between this and other LSGO wintering populations. Winter pair formation also could facilitate interbreeding with sympatric but morphologically differentiated Greater Snow Geese (C. c. atlantica; GSGO).We sequenced 658 bp of the mitochondrial DNA control region for 68 Snow Geese from East Coast and Louisiana wintering populations to examine the level of genetic differentiation among populations and subspecies. We found no evidence for genetic differentiation between LSGO populations but, consistent with morphological differences, LSGO and GSGO were significantly differentiated. We also found a lack of genetic differentiation between different LSGO morphotypes from Louisiana. We examined available banding data and found the breeding range of Delmarva LSGO overlaps extensively with LSGO that winter in Louisiana, and documented movements between wintering populations. Our results suggest the Delmarva population of LSGO is not a unique population unit apart from Mid-Continent Snow Geese. ?? 2009 by the Wilson Ornithological Society.

Analysis of pharmacogenomic variants associated with population differentiation.

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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

Analysis of pharmacogenomic variants associated with population differentiation.

Science.gov (United States)

Yeon, Bora; Ahn, Eunyong; Kim, Kyung-Im; Kim, In-Wha; Oh, Jung Mi; Park, Taesung

2015-01-01

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 associated with

Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus.

Science.gov (United States)

Dal Grande, Francesco; Sharma, Rahul; Meiser, Anjuli; Rolshausen, Gregor; Büdel, Burkhard; Mishra, Bagdevi; Thines, Marco; Otte, Jürgen; Pfenninger, Markus; Schmitt, Imke

2017-03-31

Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments. We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction. Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation.

A complex-plane strategy for computing rotating polytropic models - Numerical results for strong and rapid differential rotation

International Nuclear Information System (INIS)

Geroyannis, V.S.

1990-01-01

In this paper, a numerical method, called complex-plane strategy, is implemented in the computation of polytropic models distorted by strong and rapid differential rotation. The differential rotation model results from a direct generalization of the classical model, in the framework of the complex-plane strategy; this generalization yields very strong differential rotation. Accordingly, the polytropic models assume extremely distorted interiors, while their boundaries are slightly distorted. For an accurate simulation of differential rotation, a versatile method, called multiple partition technique is developed and implemented. It is shown that the method remains reliable up to rotation states where other elaborate techniques fail to give accurate results. 11 refs

Plant recolonization in the Himalaya from the southeastern Qinghai-Tibetan Plateau: Geographical isolation contributed to high population differentiation.

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Cun, Yu-Zhi; Wang, Xiao-Quan

2010-09-01

The Himalaya-Hengduan Mountains region (HHM) in the southern and southeastern Qinghai-Tibetan Plateau (QTP) is considered an important reservoir and a differentiation center for temperate and alpine plants in the Cenozoic. To reveal how plants responded to the Quaternary climatic oscillations in the QTP, the phylogeographical histories of a few subalpine and alpine plants have been investigated, but nearly all studies used only uniparentally inherited cytoplasmic DNA markers, and only a couple of them included sampling from the Himalaya. In this study, range-wide genetic variation of the Himalayan hemlock (Tsuga dumosa), an important forest species in the HHM, was surveyed using DNA markers from three genomes. All markers revealed genetic depauperation in the Himalaya and richness in the Hengduan Mountains populations. Surprisingly, population differentiation of this wind-pollinated conifer is very high in all three genomes, with few common and many private nuclear gene alleles. These results, together with fossil evidence, clearly indicate that T. dumosa recolonized the Himalaya from the Hengduan Mountains before the Last Glacial Maximum (LGM), accompanied with strong founder effects, and the influence of the earlier glaciations on demographic histories of the QTP plants could be much stronger than that of the LGM. The strong population differentiation in T. dumosa could be attributed to restricted gene flow caused by the complicated topography in the HHM that formed during the uplift of the QTP, and thus sheds lights on the importance of geographical isolation in the development of high plant species diversity in this biodiversity hotspot. Copyright 2010 Elsevier Inc. All rights reserved.

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

Demographic changes and marker properties affect detection of human population differentiation

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Sanichwankul Kittipong

2007-05-01

Full Text Available Abstract Background Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats. Results Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African while both successfully distinguished Hmong from Thai and Chinese. Conclusion Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.

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

Strong contribution of immigration to local population regulation: evidence from a migratory passerine.

Science.gov (United States)

Schaub, Michael; Jakober, Hans; Stauber, Wolfgang

2013-08-01

A mechanistic understanding of the dynamics of populations requires knowledge about the variation of the underlying demographic rates and about the reasons for their variability. In geographically open populations, immigration is often necessary to prevent declines, but little is known about whether immigration can contribute to its regulation. We studied the dynamics of a Red-backed Shrike population (Lanius collurio) over 36 years in Germany with a Bayesian integrated population model. We estimated mean and temporal variability of population sizes, productivity, apparent survival, and immigration. We assessed how strongly the demographic rates were correlated with population growth to understand the demographic reasons of population change and how strongly the demographic rates were correlated with population size to identify possible density-dependent mechanisms. The shrike population varied between 35 and 74 breeding pairs but did not show a significant trend in population size over time (growth rate 1.002 +/- 0.001 [mean +/- SD]). Apparent survival of females (juveniles 0.06 +/- 0.01; adults 0.37 +/- 0.03) was lower than that of males (juveniles 0.10 +/- 0.01; adults 0.44 +/- 0.02). Immigration rates were substantial and higher in females (0.56 +/- 0.02) than in males (0.43 +/- 0.02), and average productivity was 2.76 +/- 0.14. Without immigration, the Red-backed Shrike population would have declined strongly. Immigration was the strongest driver for the number of females while local recruitment was the most important driver for the number of males. Immigration of both sexes and productivity, but not local recruitment and survival, were subject to density dependence. Density-dependent productivity was not effectively regulating the local population but may have contributed to regulate shrike populations at larger spatial scales. These findings suggest that immigration is not only an important component to prevent a geographically open population from decline

The nonlocal boundary value problems for strongly singular higher-order nonlinear functional-differential equations

Czech Academy of Sciences Publication Activity Database

Mukhigulashvili, Sulkhan

-, č. 35 (2015), s. 23-50 ISSN 1126-8042 Institutional support: RVO:67985840 Keywords : higher order functional differential equations * Dirichlet boundary value problem * strong singularity Subject RIV: BA - General Mathematics http://ijpam.uniud.it/online_issue/201535/03-Mukhigulashvili.pdf

Population genetics inference for longitudinally-sampled mutants under strong selection.

Science.gov (United States)

Lacerda, Miguel; Seoighe, Cathal

2014-11-01

Longitudinal allele frequency data are becoming increasingly prevalent. Such samples permit statistical inference of the population genetics parameters that influence the fate of mutant variants. To infer these parameters by maximum likelihood, the mutant frequency is often assumed to evolve according to the Wright-Fisher model. For computational reasons, this discrete model is commonly approximated by a diffusion process that requires the assumption that the forces of natural selection and mutation are weak. This assumption is not always appropriate. For example, mutations that impart drug resistance in pathogens may evolve under strong selective pressure. Here, we present an alternative approximation to the mutant-frequency distribution that does not make any assumptions about the magnitude of selection or mutation and is much more computationally efficient than the standard diffusion approximation. Simulation studies are used to compare the performance of our method to that of the Wright-Fisher and Gaussian diffusion approximations. For large populations, our method is found to provide a much better approximation to the mutant-frequency distribution when selection is strong, while all three methods perform comparably when selection is weak. Importantly, maximum-likelihood estimates of the selection coefficient are severely attenuated when selection is strong under the two diffusion models, but not when our method is used. This is further demonstrated with an application to mutant-frequency data from an experimental study of bacteriophage evolution. We therefore recommend our method for estimating the selection coefficient when the effective population size is too large to utilize the discrete Wright-Fisher model. Copyright © 2014 by the Genetics Society of America.

Population differentiation in allele frequencies of obesity-associated SNPs.

Science.gov (United States)

Mao, Linyong; Fang, Yayin; Campbell, Michael; Southerland, William M

2017-11-10

Obesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms). We collected a total of 225 obesity-associated SNPs from a public database. Their population-level allele frequencies were derived based on the genotype data from 1000 Genomes Project (phase 3). We used hypergeometric model to assess whether the effect allele at a given SNP is significantly enriched or depleted in each of the 26 populations surveyed in the 1000 Genomes Project with respect to the overall pooled population. Our results indicate that 195 out of 225 SNPs (86.7%) possess effect alleles significantly enriched or depleted in at least one of the 26 populations. Populations within the same continental group exhibit similar allele enrichment/depletion patterns whereas inter-continental populations show distinct patterns. Among the 225 SNPs, 15 SNPs cluster in the first intron region of the FTO gene, which is a major gene associated with body-mass index (BMI) and fat mass. African populations exhibit much smaller blocks of LD (linkage disequilibrium) among these15 SNPs while European and Asian populations have larger blocks. To estimate the cumulative effect of all variants associated with obesity, we developed the personal composite genetic risk score for obesity. Our results indicate that the East Asian populations have the lowest averages of the composite risk scores, whereas three European populations have the highest averages. In addition, the population-level average of composite genetic risk scores is significantly correlated (R 2 = 0.35, P = 0.0060) with obesity prevalence. We have detected substantial population differentiation in allele frequencies of obesity-associated SNPs. The results will help elucidate the genetic basis which may contribute to population

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

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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

Differential tolerance to nickel between Dreissena polymorpha and Dreissena rostriformis bugensis populations.

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Potet, Marine; Giambérini, Laure; Pain-Devin, Sandrine; Louis, Fanny; Bertrand, Carole; Devin, Simon

2018-01-15

Differential tolerance to stress is partly responsible for the heterogeneity of biomarker responses between populations of a sentinel species. Although currently used for freshwater biomonitoring, studies concerning inter-populational variability in tolerance to contaminants for the zebra mussel (Dreissena polymorpha) are scarce. Moreover, this well-known invader is currently replaced by another, the quagga mussel (Dreissena rostriformis bugensis). To evaluate the differential tolerance between dreissenids, several populations of both species were exposed to a high concentration of nickel. A LT 50 (time when 50% of individuals were dead) was established for each population. Biomarker responses and internal nickel concentration were also measured, to link tolerance with physiological status. Results evidenced that D. polymorpha populations are more heterogeneous and more tolerant than D. r. bugensis ones. For D. polymorpha populations only, LT 50 values were positively correlated with the nickel contamination in situ, with higher anti-oxidative defences and a higher Integrated Biomarker Response value in the field. Such findings may be explained by local adaptation and invasion dynamic within each species. The significance of this differential tolerance when using biomarker responses for biomonitoring purposes is thus discussed.

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

Science.gov (United States)

Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

2018-01-01

Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

Science.gov (United States)

Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

2014-03-20

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

[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.

Articular cartilage-derived cells hold a strong osteogenic differentiation potential in comparison to mesenchymal stem cells in vitro

International Nuclear Information System (INIS)

Salamon, Achim; Jonitz-Heincke, Anika; Adam, Stefanie; Rychly, Joachim; Müller-Hilke, Brigitte; Bader, Rainer; Lochner, Katrin; Peters, Kirsten

2013-01-01

Cartilaginous matrix-degenerative diseases like osteoarthritis (OA) are characterized by gradual cartilage erosion, and also by increased presence of cells with mesenchymal stem cell (MSC) character within the affected tissues. Moreover, primary chondrocytes long since are known to de-differentiate in vitro and to be chondrogenically re-differentiable. Since both findings appear to conflict with each other, we quantitatively assessed the mesenchymal differentiation potential of OA patient cartilage-derived cells (CDC) towards the osteogenic and adipogenic lineage in vitro and compared it to that of MSC isolated from adipose tissue (adMSC) of healthy donors. We analyzed expression of MSC markers CD29, CD44, CD105, and CD166, and, following osteogenic and adipogenic induction in vitro, quantified their expression of osteogenic and adipogenic differentiation markers. Furthermore, CDC phenotype and proliferation were monitored. We found that CDC exhibit an MSC CD marker expression pattern similar to adMSC and a similar increase in proliferation rate during osteogenic differentiation. In contrast, the marked reduction of proliferation observed during adipogenic differentiation of adMSC was absent in CDC. Quantification of differentiation markers revealed a strong osteogenic differentiation potential for CDC, however almost no capacity for adipogenic differentiation. Since in the pathogenesis of OA, cartilage degeneration coincides with high bone turnover rates, the high osteogenic differentiation potential of OA patient-derived CDC may affect clinical therapeutic regimens aiming at autologous cartilage regeneration in these patients. - Highlights: • We analyze the mesenchymal differentiation capacity of cartilage-derived cells (CDC). • CDC express mesenchymal stem cell (MSC) markers CD29, CD44, CD105, and CD166. • CDC and MSC proliferation is reduced in adipogenesis and increased in osteogenesis. • Adipogenic differentiation is virtually absent in CDC, but

Articular cartilage-derived cells hold a strong osteogenic differentiation potential in comparison to mesenchymal stem cells in vitro

Energy Technology Data Exchange (ETDEWEB)

Salamon, Achim, E-mail: achim.salamon@med.uni-rostock.de [Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany); Jonitz-Heincke, Anika, E-mail: anika.jonitz@med.uni-rostock.de [Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Doberaner Straße 142, D-18057 Rostock (Germany); Adam, Stefanie, E-mail: stefanie.adam@med.uni-rostock.de [Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany); Rychly, Joachim, E-mail: joachim.rychly@med.uni-rostock.de [Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany); Müller-Hilke, Brigitte, E-mail: brigitte.mueller-hilke@med.uni-rostock.de [Institute of Immunology, Rostock University Medical Center, Schillingallee 68, D-18057 Rostock (Germany); Bader, Rainer, E-mail: rainer.bader@med.uni-rostock.de [Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Doberaner Straße 142, D-18057 Rostock (Germany); Lochner, Katrin, E-mail: katrin.lochner@med.uni-rostock.de [Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Doberaner Straße 142, D-18057 Rostock (Germany); Peters, Kirsten, E-mail: kirsten.peters@med.uni-rostock.de [Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany)

2013-11-01

Cartilaginous matrix-degenerative diseases like osteoarthritis (OA) are characterized by gradual cartilage erosion, and also by increased presence of cells with mesenchymal stem cell (MSC) character within the affected tissues. Moreover, primary chondrocytes long since are known to de-differentiate in vitro and to be chondrogenically re-differentiable. Since both findings appear to conflict with each other, we quantitatively assessed the mesenchymal differentiation potential of OA patient cartilage-derived cells (CDC) towards the osteogenic and adipogenic lineage in vitro and compared it to that of MSC isolated from adipose tissue (adMSC) of healthy donors. We analyzed expression of MSC markers CD29, CD44, CD105, and CD166, and, following osteogenic and adipogenic induction in vitro, quantified their expression of osteogenic and adipogenic differentiation markers. Furthermore, CDC phenotype and proliferation were monitored. We found that CDC exhibit an MSC CD marker expression pattern similar to adMSC and a similar increase in proliferation rate during osteogenic differentiation. In contrast, the marked reduction of proliferation observed during adipogenic differentiation of adMSC was absent in CDC. Quantification of differentiation markers revealed a strong osteogenic differentiation potential for CDC, however almost no capacity for adipogenic differentiation. Since in the pathogenesis of OA, cartilage degeneration coincides with high bone turnover rates, the high osteogenic differentiation potential of OA patient-derived CDC may affect clinical therapeutic regimens aiming at autologous cartilage regeneration in these patients. - Highlights: • We analyze the mesenchymal differentiation capacity of cartilage-derived cells (CDC). • CDC express mesenchymal stem cell (MSC) markers CD29, CD44, CD105, and CD166. • CDC and MSC proliferation is reduced in adipogenesis and increased in osteogenesis. • Adipogenic differentiation is virtually absent in CDC, but

The focal boundary value problem for strongly singular higher-order nonlinear functional-differential equations

Czech Academy of Sciences Publication Activity Database

Mukhigulashvili, Sulkhan; Půža, B.

2015-01-01

Roč. 2015, January (2015), s. 17 ISSN 1687-2770 Institutional support: RVO:67985840 Keywords : higher order nonlinear functional-differential equations * two-point right-focal boundary value problem * strong singularity Subject RIV: BA - General Mathematics Impact factor: 0.642, year: 2015 http://link.springer.com/article/10.1186%2Fs13661-014-0277-1

Periodic solutions of nonautonomous differential systems modeling obesity population

International Nuclear Information System (INIS)

Arenas, Abraham J.; Gonzalez-Parra, Gilberto; Jodar, Lucas

2009-01-01

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.

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.

Synergy between Allopatry and Ecology in Population Differentiation and Speciation

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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.

Delay differential systems for tick population dynamics.

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Fan, Guihong; Thieme, Horst R; Zhu, Huaiping

2015-11-01

Ticks play a critical role as vectors in the transmission and spread of Lyme disease, an emerging infectious disease which can cause severe illness in humans or animals. To understand the transmission dynamics of Lyme disease and other tick-borne diseases, it is necessary to investigate the population dynamics of ticks. Here, we formulate a system of delay differential equations which models the stage structure of the tick population. Temperature can alter the length of time delays in each developmental stage, and so the time delays can vary geographically (and seasonally which we do not consider). We define the basic reproduction number [Formula: see text] of stage structured tick populations. The tick population is uniformly persistent if [Formula: see text] and dies out if [Formula: see text]. We present sufficient conditions under which the unique positive equilibrium point is globally asymptotically stable. In general, the positive equilibrium can be unstable and the system show oscillatory behavior. These oscillations are primarily due to negative feedback within the tick system, but can be enhanced by the time delays of the different developmental stages.

[Genetic differentiation of Isaria farinosa populations in Anhui Province of East China].

Science.gov (United States)

Sun, Zhao-Hong; Luan, Feng-Gang; Zhang, Da-Min; Chen, Ming-Jun; Wang, Bin; Li, Zeng-Zhi

2011-11-01

Isaria farinosa is an important entomopathogenic fungus. By using ISSR, this paper studied the genetic heterogeneity of six I. farinosa populations at different localities of Anhui Province, East China. A total of 98.5% polymorphic loci were amplified with ten polymorphic primers, but the polymorphism at population level varied greatly, within the range of 59.6%-93.2%. The genetic differentiation index (G(st)) between the populations based on Nei's genetic heterogenesis analysis was 0.3365, and the gene flow (N(m)) was 0.4931. The genetic differentiation between the populations was lower than that within the populations, suggesting that the genetic variation of I. farinosa mainly come from the interior of the populations. The UPGMA clustering based on the genetic similarities between the isolates revealed that the Xishan population was monophylectic, while the other five populations were polyphylectic, with the Yaoluoping population being the most heterogenic and the Langyashan population being the least heterogenic. No correlations were observed between the geographic distance and the genetic distance of the populations. According to the UPGMA clustering based on the genetic distance between the populations, the six populations were classified into three groups, and this classification was accorded with the clustering based on geographic environment, suggesting the effects of environmental heterogeneity on the population heterogeneity.

Declines in populations of Salix caprea L.during forest regeneration after strong herbivore pressure

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Janusz B. Faliński

2014-01-01

Full Text Available Communities of broadleaved forest subject to strong pressure from large herbivores underwent degeneration. The relief of this pressure led to regeneration of the community, in which an important role was played by the sallow Salix caprea and other light-seeded pioneer species of tree (Populus tremula, Betula pendula and B. pubescens. Regeneration involving Salix caprea proceeded following the conservatorial protection of the degenerate stands in a reserve and later in Białowieża National Park. The emergence and development of the population of Salix caprea proceeded following the invasion of spruce, which coincided with the period of enhanced animal pressure on broadleaved forest. Salix caprea filled all the gaps in the tree stand arising as a result of the destruction of trees and undergrowth by herbivores (in the years 1892-1915. It also appeared en masse on old, at that time unforested, clearings and felled areas. In these places, Salix caprea created very abundant populations, with particular trees being in good condition, with a habit typical of forest trees and attaining considerable heights. The majority of trees were 50-60 years old at the time of death, although individuals reached 74 years of age. The process of extinction of the sallow population - observed over 19 years on permanent plots and fixed trees - proceeded very quickly, especially in the first decade of observation. It led to the almost complete disappearance of sallow for the forest communities of Białowieża National Park. The death of individual trees is preceded by impairment of their health and reduced annual increments in the 4-9 last years of life. The extinction of the population is associated with the loss of its primary phenological differentiation and with a change in the sex structure of the population from a prevalence of female trees to a near even distribution of the two sexes. The development of the populations of permanent constituents of the forest

Strongly increasing solutions of cyclic systems of second order differential equations with power-type nonlinearities

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Jaroslav Jaroš

2015-01-01

Full Text Available We consider \\(n\\-dimensional cyclic systems of second order differential equations \\[(p_i(t|x_{i}'|^{\\alpha_i -1}x_{i}'' = q_{i}(t|x_{i+1}|^{\\beta_i-1}x_{i+1},\\] \\[\\quad i = 1,\\ldots,n, \\quad (x_{n+1} = x_1 \\tag{\\(\\ast\\}\\] under the assumption that the positive constants \\(\\alpha_i\\ and \\(\\beta_i\\ satisfy \\(\\alpha_1{\\ldots}\\alpha_n \\gt \\beta_1{\\ldots}\\beta_n\\ and \\(p_i(t\\ and \\(q_i(t\\ are regularly varying functions, and analyze positive strongly increasing solutions of system (\\(\\ast\\ in the framework of regular variation. We show that the situation for the existence of regularly varying solutions of positive indices for (\\(\\ast\\ can be characterized completely, and moreover that the asymptotic behavior of such solutions is governed by the unique formula describing their order of growth precisely. We give examples demonstrating that the main results for (\\(\\ast\\ can be applied to some classes of partial differential equations with radial symmetry to acquire accurate information about the existence and the asymptotic behavior of their radial positive strongly increasing solutions.

[Matrimonial radius and anthropologic differentiation of the population of the Peloponnese, Greece].

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Pitsios, T K

1983-09-01

Mean matrimonial radius (MMR) and mean breeding radius (MBR) were studied in the population of the Peloponnese (Greece). The historical and geographical causes of these important genetical variables are discussed considering, too, their effects on the anthropological differentiation of this population.

The evolution of strong reciprocity: cooperation in heterogeneous populations.

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Bowles, Samuel; Gintis, Herbert

2004-02-01

How do human groups maintain a high level of cooperation despite a low level of genetic relatedness among group members? We suggest that many humans have a predisposition to punish those who violate group-beneficial norms, even when this imposes a fitness cost on the punisher. Such altruistic punishment is widely observed to sustain high levels of cooperation in behavioral experiments and in natural settings. We offer a model of cooperation and punishment that we call STRONG RECIPROCITY: where members of a group benefit from mutual adherence to a social norm, strong reciprocators obey the norm and punish its violators, even though as a result they receive lower payoffs than other group members, such as selfish agents who violate the norm and do not punish, and pure cooperators who adhere to the norm but free-ride by never punishing. Our agent-based simulations show that, under assumptions approximating likely human environments over the 100000 years prior to the domestication of animals and plants, the proliferation of strong reciprocators when initially rare is highly likely, and that substantial frequencies of all three behavioral types can be sustained in a population. As a result, high levels of cooperation are sustained. Our results do not require that group members be related or that group extinctions occur.

Rapid evolution leads to differential population dynamics and top-down control in resurrected Daphnia populations.

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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.

Parameter Estimates in Differential Equation Models for Population Growth

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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,…

Reconstructing human pancreatic differentiation by mapping specific cell populations during development

DEFF Research Database (Denmark)

Ramond, Cyrille; Glaser, Nicolas; Berthault, Claire

2017-01-01

. Endocrine maturation progresses by up-regulating SUSD2 and lowering ECAD levels. Finally, in vitro differentiation of pancreatic endocrine cells derived from human pluripotent stem cells mimics key in vivo events. Our work paves the way to extend our understanding of the origin of mature human pancreatic......Information remains scarce on human development compared to animal models. Here, we reconstructed human fetal pancreatic differentiation using cell surface markers. We demonstrate that at 7weeks of development, the glycoprotein 2 (GP2) marks a multipotent cell population that will differentiate...... cell types and how such lineage decisions are regulated....

Epigenetic Differentiation of Natural Populations of Lilium bosniacum Associated with Contrasting Habitat Conditions.

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Zoldoš, Vlatka; Biruš, Ivan; Muratovic, Edina; Šatovic, Zlatko; Vojta, Aleksandar; Robin, Odile; Pustahija, Fatima; Bogunic, Faruk; Vicic Bockor, Vedrana; Siljak-Yakovlev, Sonja

2018-01-01

Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses revealed that the three populations did not differentiate genetically, but were clearly separated in three distinct clusters according to DNA methylation profiles. Principal coordinate analysis showed that overall epigenetic variation was closely related to habitat conditions. A new methylation-sensitive amplification polymorphism scoring approach allowed identification of mainly unmethylated (φST = 0.190) and fully CpG methylated (φST = 0.118) subepiloci playing a role in overall population differentiation, in comparison with hemimethylated sites (φST = 0.073). In addition, unusual rDNA repatterning and the presence of B chromosomes bearing 5S rDNA loci were recorded in the population growing on serpentine soil, suggesting dynamic chromosome rearrangements probably linked to global genome demethylation, which might have reactivated some mobile elements. We discuss our results considering our earlier data on morphology and leaf anatomy of several L. bosniacum populations, and suggest a possible role of epigenetics as a key element in population differentiation associated with environmental stress in these particular lily populations. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Rare sugar D-allose strongly induces thioredoxin-interacting protein and inhibits osteoclast differentiation in Raw264 cells.

Science.gov (United States)

Yamada, Kana; Noguchi, Chisato; Kamitori, Kazuyo; Dong, Youyi; Hirata, Yuko; Hossain, Mohammad A; Tsukamoto, Ikuko; Tokuda, Masaaki; Yamaguchi, Fuminori

2012-02-01

Oxidative stress modulates the osteoclast differentiation via redox systems, and thioredoxin 1 (Trx) promotes the osteoclast formation by regulating the activity of transcription factors. The function of Trx is known to be regulated by its binding partner, thioredoxin-interacting protein (TXNIP). We previously reported that the expression of TXNIP gene is strongly induced by a rare sugar D-allose. In this study, we tested the hypothesis that D-allose could inhibit the osteoclast differentiation by regulating the Trx function. We used a murine Raw264 cell line that differentiates to the osteoclast by the receptor activator of nuclear factor-κB ligand (RANKL) treatment. The effect of sugars was evaluated by tartrate-resistant acid phosphatase staining. The expression and localization of TXNIP and Trx protein were examined by Western blotting and immunohistochemisty. The activity of the nuclear factor-κB, nuclear factor of activated T cells, and activator protein 1 transcription factors was measured by the luciferase reporter assay. The addition of D-allose (25 mmol/L) inhibited the osteoclast differentiation down to 9.53% ± 1.27% of a receptor activator of nuclear factor-κB ligand-only treatment. During the osteoclast differentiation, a significant increase of TNXIP was observed by D-allose treatment. The immunohistochemical analysis showed that both Trx and TXNIP existed in the nucleus in preosteoclasts and osteoclasts. Overexpression of TXNIP by plasmid transfection also inhibited the osteoclast formation, indicating the functional importance of TXNIP for the osteoclast differentiation. Transcriptional activity of the activator protein 1, nuclear factor-κB, and nuclear factor of activated T cells, known to be modulated by Trx, were inhibited by D-allose. In conclusion, our data indicate that D-allose is a strong inhibitor of the osteoclast differentiation, and this effect could be caused by TXNIP induction and a resulting inhibition of the Trx function

Patterns of population differentiation of candidate genes for cardiovascular disease

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Ding Keyue

2007-07-01

Full Text Available Abstract Background The basis for ethnic differences in cardiovascular disease (CVD susceptibility is not fully understood. We investigated patterns of population differentiation (FST of a set of genes in etiologic pathways of CVD among 3 ethnic groups: Yoruba in Nigeria (YRI, Utah residents with European ancestry (CEU, and Han Chinese (CHB + Japanese (JPT. We identified 37 pathways implicated in CVD based on the PANTHER classification and 416 genes in these pathways were further studied; these genes belonged to 6 biological processes (apoptosis, blood circulation and gas exchange, blood clotting, homeostasis, immune response, and lipoprotein metabolism. Genotype data were obtained from the HapMap database. Results We calculated FST for 15,559 common SNPs (minor allele frequency ≥ 0.10 in at least one population in genes that co-segregated among the populations, as well as an average-weighted FST for each gene. SNPs were classified as putatively functional (non-synonymous and untranslated regions or non-functional (intronic and synonymous sites. Mean FST values for common putatively functional variants were significantly higher than FST values for nonfunctional variants. A significant variation in FST was also seen based on biological processes; the processes of 'apoptosis' and 'lipoprotein metabolism' showed an excess of genes with high FST. Thus, putative functional SNPs in genes in etiologic pathways for CVD show greater population differentiation than non-functional SNPs and a significant variance of FST values was noted among pairwise population comparisons for different biological processes. Conclusion These results suggest a possible basis for varying susceptibility to CVD among ethnic groups.

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

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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.

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

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Carlos M Herrera

Full Text Available 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.

Population Differentiation and Hybridisation of Australian Snubfin (Orcaella heinsohni) and Indo-Pacific Humpback (Sousa chinensis) Dolphins in North-Western Australia

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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 (F ST = 0.05–0.09; P<0.001) and a 422 bp sequence of the mitochondrial control region (F ST = 0.50–0.70; P<0.001). The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00–0.06) to 0.13 (0.03–0.24). These are the first estimates of genetic 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

Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni and Indo-Pacific humpback (Sousa chinensis dolphins in north-western Australia.

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Alexander M Brown

Full Text Available 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; P<0.001 and a 422 bp sequence of the mitochondrial control region (FST = 0.50-0.70; P<0.001. The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00-0.06 to 0.13 (0.03-0.24. These are the first estimates of genetic 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

Direct characterization of chaotic and stochastic dynamics in a population model with strong periodicity

International Nuclear Information System (INIS)

Tung Wenwen; Qi Yan; Gao, J.B.; Cao Yinhe; Billings, Lora

2005-01-01

In recent years it has been increasingly recognized that noise and determinism may have comparable but different influences on population dynamics. However, no simple analysis methods have been introduced into ecology which can readily characterize those impacts. In this paper, we study a population model with strong periodicity and both with and without noise. The noise-free model generates both quasi-periodic and chaotic dynamics for certain parameter values. Due to the strong periodicity, however, the generated chaotic dynamics have not been satisfactorily described. The dynamics becomes even more complicated when there is noise. Characterizing the chaotic and stochastic dynamics in this model thus represents a challenging problem. Here we show how the chaotic dynamics can be readily characterized by the direct dynamical test for deterministic chaos developed by [Gao JB, Zheng ZM. Europhys. Lett. 1994;25:485] and how the influence of noise on quasi-periodic motions can be characterized as asymmetric diffusions wandering along the quasi-periodic orbit. It is hoped that the introduced methods will be useful in studying other population models as well as population time series obtained both in field and laboratory experiments

Microsatellite data suggest significant population structure and differentiation within the malaria vector Anopheles darlingi in Central and South America

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Achee Nicole L

2008-03-01

Full Text Available Abstract Background Anopheles darlingi is the most important malaria vector in the Neotropics. An understanding of A. darlingi's population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5–8 microsatellite loci. Results We found high levels of polymorphism for all of the Amazonian populations (mean RS = 7.62, mean HO = 0.742, and low levels for the Belize and Guatemalan populations (mean RS = 4.3, mean HO = 0.457. The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (FST = 0.1859 – 0.3901, P DA and FST distance-based trees illustrated the main division to be between Central America and Amazonia. Conclusion We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in Ne among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within A. darlingi corresponds to two white gene genotypes between Amazonia (genotype 1

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

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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.

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

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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.

Variation in sclerophylly among Iberian populations of Quercus coccifera L. is associated with genetic differentiation across contrasting environments.

Science.gov (United States)

Rubio de Casas, R; Vargas, P; Pérez-Corona, E; Cano, E; Manrique, E; García-Verdugo, C; Balaguer, L

2009-05-01

Evergreen oaks are an emblematic element of the Mediterranean vegetation and have a leaf phenotype that seems to have remained unchanged since the Miocene. We hypothesise that variation of the sclerophyll phenotype among Iberian populations of Quercus coccifera is partly due to an ulterior process of ecotypic differentiation. We analysed the genetic structure of nine Iberian populations using ISSR fingerprints, and their leaf phenotypes using mean and intracanopy plasticity values of eight morphological (leaf angle, area, spinescence, lobation and specific area) and biochemical traits (VAZ pool, chlorophyll and beta-carotene content). Climate and soil were also characterised at the population sites. Significant genetic and phenotypic differences were found among populations and between NE Iberia and the rest of the populations of the peninsula. Mean phenotypes showed a strong and independent correlation with both genetic and geographic distances. Northeastern plants were smaller, less plastic, with smaller, spinier and thicker leaves, a phenotype consistent with the stressful conditions that prevailed in the steppe environments of the refugia within this geographic area during glaciations. These genetic, phenotypic, geographic and environmental patterns are consistent with previously reported palaeoecological and common evidence. Such consistency leads us to conclude that there has been a Quaternary divergence within the sclerophyllous syndrome that was at least partially driven by ecological factors.

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

Science.gov (United States)

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

[Genetic structure, subdivision, and population differentiation in Stankewiczii pine Pinus stankewiczii (Sukacz.) Fomin from Mountain Crimea].

Science.gov (United States)

Korshikov, I I; Gorlova, E M

2006-06-01

In order to analyze the genetic structure, subdivision and differentiation within and between two small isolated populations of the Crimea relict endemic, Pinus stankewiczii (Sukacz.) Fomin, electrophoretic analysis of the isozyme variation at nine enzymatic systems was carried out using 183 oldest trees. It was demonstrated that in populations of P. stankewiczii, 80% of the genes were in polymorphic state. Each tree was heterozygous at 19.1% loci, and at 21.6% loci in artificial 50-year-old plantation. The genetic structure of two populations was less differentiated (DN = 0.006), compared to their individual localities (DN = 0.008-0.009). Within-population subdivision of the diffusely dispersed populations was higher (FST-GST = 1.8-2.0%) than that of the populations themselves (0.8%).

Strong persistent growth differences govern individual performance and population dynamics in a tropical forest understorey palm

NARCIS (Netherlands)

Jansen, M.; Zuidema, P.A.; Anten, N.P.R.; Martínez-Ramos, M.

2012-01-01

1. Persistent variation in growth rate between individual plants can have strong effects on population dynamics as fast growers reach the reproductive size at an earlier age and thus potentially contribute more to population growth than slow growers. In tropical forests, such persistent growth

Optimization of strong and weak coordinates

NARCIS (Netherlands)

Swart, M.; Bickelhaupt, F.M.

2006-01-01

We present a new scheme for the geometry optimization of equilibrium and transition state structures that can be used for both strong and weak coordinates. We use a screening function that depends on atom-pair distances to differentiate strong coordinates from weak coordinates. This differentiation

Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population

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Larsson Mikael

2010-02-01

Full Text Available Abstract Background Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird. Results The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers. Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair's hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching. Conclusions Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.

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.

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

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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

Mesoscopic fluctuations of the population of a qubit in a strong alternating field

Energy Technology Data Exchange (ETDEWEB)

Denisenko, M. V., E-mail: mar.denisenko@gmail.com; Satanin, A. M. [Lobachevsky State University of Nizhny Novgorod (Russian Federation)

2016-12-15

Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau–Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of the population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.

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.

Linking Diversity and Differentiation

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Hans-Rolf Gregorius

2010-03-01

Full Text Available Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective numbers of trait states (types. Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered.

Genetic diversity and differentiation of Mongolian indigenous cattle populations

Energy Technology Data Exchange (ETDEWEB)

Lkhagva, B [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya) and Mongolian State Agricultural University, Zaisan, Ulaanbaatar 210153 (Mongolia); Ochieng, J W; Hanotte, O; Jianlin, H [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya); Yoon, D H [National Livestock Research Institute, RDA, 441-350, Suwon (Korea)

2003-07-01

Livestock production plays an important role in Mongolian economy. Over the last decade it has contributed to around 80-90% of the gross domestic agricultural products and to 30% of the revenues generated from exportations. Cattle is one of the five traditional and most important livestock species of Mongolia together with horse, sheep, goat and camel. Out of a total of 1.57 millions Mongolian cattle, 1.55 millions supposedly belong to three indigenous Bos taurus cattle breeds, namely Mongol, Selenge and Khalkhun Golun, all herded under extensive pastoral systems. Indigenous Mongolian cattle are generally small but look sturdy and strong. They have a well-off coat of hair, solid forward looking shoulders and short stubby snouts, and they are used for meat, milk and transport. Beef production contributes to 30% of the total meat supply in Mongolia. The Mongol breed is by the far the commonest with 1.53 million animals and it is found almost throughout the country. The Selenge breed, found in Selenge province and numbering 9000 heads, was developed in middle of the 20th century by crossing the Kazakh Whiteheaded with the local Mongol cattle. The Khalkhun Golun breed was developed from local Mongol cattle and it is distributed in Eastern and Suhbaatar provinces with about 10,000 heads. Until now, to the best of our knowledge, only a single population of Mongolian cattle has been studied with microsatellite DNA markers and no information is available on the genetic relationship between the Mongolian indigenous cattle breeds. In this study, we collected samples from two populations of the Mongol cattle (sampled at Ikhtamir soum in North Hangay province and Tsogt soum in Govi Altay province) and one population of the Khalkhun Golun cattle (sampled at Tumentsogt soum in Suhbaatar province). Samples were characterised with nine microsatellite markers MGTG4B, ILSTS005, ILSTS006, ILSTS008, ILSTS023, ILSTS028, ILSTS036, ILSTS050 and ILSTS103. To assess the genetic diversity

Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

Science.gov (United States)

Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

2015-09-01

How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

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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.

NIDI scenario. Strong population decline in China

OpenAIRE

de Beer, J.A.A.

2016-01-01

United Nations projections assume that by the end of this century one third of the world population will live in India, China or Nigeria. While population growth in India will slow down and the population size of China will decline, population growth in Nigeria will accelerate. A new NIDI scenario projects less population growth in Nigeria and sharp population decline in China.

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

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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.

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...... 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......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...

On an nth-order infinitesimal generator and time-dependent operator differential equation with a strongly almost periodic solution

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Aribindi Satyanarayan Rao

2002-01-01

Full Text Available In a Banach space, if u is a Stepanov almost periodic solution of a certain nth-order infinitesimal generator and time-dependent operator differential equation with a Stepanov almost periodic forcing function, then u,u′,…,u (n−2 are all strongly almost periodic and u (n−1 is weakly almost periodic.

Evidence of Recent Intricate Adaptation in Human Populations.

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Leeyoung Park

Full Text Available Recent human adaptations have shaped population differentiation in genomic regions containing putative functional variants, mostly located in predicted regulatory elements. However, their actual functionalities and the underlying mechanism of recent adaptation remain poorly understood. In the current study, regions of genes and repeats were investigated for functionality depending on the degree of population differentiation, FST or ΔDAF (a difference in derived allele frequency. The high FST in the 5´ or 3´ untranslated regions (UTRs, in particular, confirmed that population differences arose mainly from differences in regulation. Expression quantitative trait loci (eQTL analyses using lymphoblastoid cell lines indicated that the majority of the highly population-specific regions represented cis- and/or trans-eQTL. However, groups having the highest ΔDAFs did not necessarily have higher proportions of eQTL variants; in these groups, the patterns were complex, indicating recent intricate adaptations. The results indicated that East Asian (EAS and European populations (EUR experienced mutual selection pressures. The mean derived allele frequency of the high ΔDAF groups suggested that EAS and EUR underwent strong adaptation; however, the African population in Africa (AFR experienced slight, yet broad, adaptation. The DAF distributions of variants in the gene regions showed clear selective pressure in each population, which implies the existence of more recent regulatory adaptations in cells other than lymphoblastoid cell lines. In-depth analysis of population-differentiated regions indicated that the coding gene, RNF135, represented a trans-regulation hotspot via cis-regulation by the population-specific variants in the region of selective sweep. Together, the results provide strong evidence of actual intricate adaptation of human populations via regulatory manipulation.

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

Science.gov (United States)

Palková, Zdena; Wilkinson, Derek; Váchová, Libuše

2014-02-01

Over the past decade, it has become evident that similarly to cells forming metazoan tissues, yeast cells have the ability to differentiate and form specialized cell types. Examples of yeast cellular differentiation have been identified both in yeast liquid cultures and within multicellular structures occupying solid surfaces. Most current knowledge on different cell types comes from studies of the spatiotemporal internal architecture of colonies developing on various media. With a few exceptions, yeast cell differentiation often concerns nongrowing, stationary-phase cells and leads to the formation of cell subpopulations differing in stress resistance, cell metabolism, respiration, ROS production, and others. These differences can affect longevity of particular subpopulations. In contrast to liquid cultures, where various cell types are dispersed within stationary-phase populations, cellular differentiation depends on the specific position of particular cells within multicellular colonies. Differentiated colonies, thus, resemble primitive multicellular organisms, in which the gradients of certain compounds and the position of cells within the structure affect cellular differentiation. In this review, we summarize and compare the properties of diverse types of differentiated chronologically aging yeast cells that have been identified in colonies growing on different media, as well as of those found in liquid cultures. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

DEFF Research Database (Denmark)

Hansen, Michael Møller; Mensberg, Karen-Lise Dons

2009-01-01

, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943-1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pair-wise F-ST of 0.047 and 0.053). By analysing...... a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals...... nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor...

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

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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

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...

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

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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

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

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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

Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

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Rong Chen

Full Text Available 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

NIDI scenario. Strong population decline in China

NARCIS (Netherlands)

de Beer, J.A.A.

2016-01-01

United Nations projections assume that by the end of this century one third of the world population will live in India, China or Nigeria. While population growth in India will slow down and the population size of China will decline, population growth in Nigeria will accelerate. A new NIDI scenario

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

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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.

Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

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Lesser, M R; Parchman, T L; Jackson, S T

2013-05-01

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

Reduction of structured population models to threshold-type delay equations and functional differential equations: A case study

Energy Technology Data Exchange (ETDEWEB)

Smith, H.L. (Arizona State Univ., Tempe (United States))

1993-01-01

It is shown by way of a simple example that certain structured population models lead naturally to differential delay equations of the threshold type and that these equations can be transformed in a natural way to functional differential equations. The model examined can be viewed as a model of competition between adults and juveniles of a single population. The results indicate the possibility that this competition leads to instability. 28 refs., 2 figs.

Genetic differentiation and population structure of five ethnic groups of Punjab (North-West India).

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Singh, Gagandeep; Talwar, Indu; Sharma, Rubina; Matharoo, Kawaljit; Bhanwer, A J S

2016-12-01

The state of Punjab in the North-West part of India has acted as the main passage for all the major human invasions into the Indian subcontinent. It has resulted in the mixing of foreign gene pool into the local populations, which led to an extensive range of genetic diversity and has influenced the genetic structure of populations in Punjab, North-West India. The present study was conducted to examine the genetic structure, relationships, and extent of genetic differentiation in five Indo-European speaking ethnic groups of Punjab. A total of 1021 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris, and Scheduled castes were analyzed for four human-specific Ins/Del polymorphic loci (ACE, APO, PLAT, and D1) and three restriction fragment length polymorphisms ESR (PvuII), LPL (PvuII), and T2 (MspI) using Polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. The frequency of the Alu insertion at APO locus was observed to exhibit the highest value (82.6-96.3 %), whereas D1 exhibited the lowest (26.5-45.6 %) among all the ethnic groups. The average heterozygosity among the studied populations ranged from 0.3816 in Banias to 0.4163 in Khatris. The F ST values ranged from 0.0418 to 0.0033 for the PLAT and LPL loci, respectively, with an average value being 0.0166. Phylogenetic analysis revealed that Banias and Khatris are genetically closest to each other. The Jat Sikhs are genetically close to Brahmins and are distant from the Banias. The Jat Sikhs, Banias, Brahmins, and Khatris are genetically very distant from the Scheduled castes. Overall, Uniform allele frequency distribution patterns, high average heterozygosity values, and a small degree of genetic differentiation in this study suggest a genetic proximity among the selected populations. A low level of genetic differentiation was observed in the studied population groups indicating that genetic drift might have been small or negligible in shaping

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

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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.

Population differentiation in the context of Holocene climate change for a migratory marine species, the southern elephant seal.

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Corrigan, L J; Fabiani, A; Chauke, L F; McMahon, C R; de Bruyn, M; Bester, M N; Bastos, A; Campagna, C; Muelbert, M M C; Hoelzel, A R

2016-09-01

Understanding observed patterns of connectivity requires an understanding of the evolutionary processes that determine genetic structure among populations, with the most common models being associated with isolation by distance, allopatry or vicariance. Pinnipeds are annual breeders with the capacity for extensive range overlap during seasonal migrations, establishing the potential for the evolution of isolation by distance. Here, we assess the pattern of differentiation among six breeding colonies of the southern elephant seal, Mirounga leonina, based on mtDNA and 15 neutral microsatellite DNA markers, and consider measures of their demography and connectivity. We show that all breeding colonies are genetically divergent and that connectivity in this highly mobile pinniped is not strongly associated with geographic distance, but more likely linked to Holocene climate change and demographic processes. Estimates of divergence times between populations were all after the last glacial maximum, and there was evidence for directional migration in a clockwise pattern (with the prevailing current) around the Antarctic. We discuss the mechanisms by which climate change may have contributed to the contemporary genetic structure of southern elephant seal populations and the broader implications. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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

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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.

An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

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Conwill, Arolyn; Yurtsev, Eugene; Gore, Jeff

2014-03-01

A common mechanism of antibiotic resistance in bacteria involves the production of an enzyme that inactivates the antibiotic. By inactivating the antibiotic, resistant cells can protect other cells in the population that would otherwise be sensitive to the drug. In a multidrug environment, an obligatory mutualism arises because populations of different strains rely on each other to breakdown antibiotics in the environment. Here, we experimentally track the population dynamics of two E. coli strains in the presence of two different antibiotics: ampicillin and chloramphenicol. Together the strains are able to grow in antibiotic concentrations that inhibit growth of either one of the strains alone. Although mutualisms are often thought to stabilize population dynamics, we observe strong oscillatory dynamics even when there is long-term coexistence between the two strains. We expect that our results will provide insight into the evolution of antibiotic resistance and, more generally, the evolutionary origin of phenotypic diversity, cooperation, and ecological stability.

Strong selection during the last millennium for African ancestry in the admixed population of Madagascar.

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Pierron, Denis; Heiske, Margit; Razafindrazaka, Harilanto; Pereda-Loth, Veronica; Sanchez, Jazmin; Alva, Omar; Arachiche, Amal; Boland, Anne; Olaso, Robert; Deleuze, Jean-Francois; Ricaut, Francois-Xavier; Rakotoarisoa, Jean-Aimé; Radimilahy, Chantal; Stoneking, Mark; Letellier, Thierry

2018-03-02

While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

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.

The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.

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Nordborg, Magnus; Innan, Hideki

2003-03-01

A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae).

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Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M; Marcet, Paula L

2013-12-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. Copyright © 2013. Published by Elsevier B.V.

RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

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Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

2017-02-08

Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of F ST and R ST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

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

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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.

Strong spatial genetic structure in five tropical Piper species: should the Baker–Fedorov hypothesis be revived for tropical shrubs?

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Lasso, E; Dalling, J W; Bermingham, E

2011-01-01

Fifty years ago, Baker and Fedorov proposed that the high species diversity of tropical forests could arise from the combined effects of inbreeding and genetic drift leading to population differentiation and eventually to sympatric speciation. Decades of research, however have failed to support the Baker–Fedorov hypothesis (BFH), and it has now been discarded in favor of a paradigm where most trees are self-incompatible or strongly outcrossing, and where long-distance pollen dispersal prevents population drift. Here, we propose that several hyper-diverse genera of tropical herbs and shrubs, including Piper (>1,000 species), may provide an exception. Species in this genus often have aggregated, high-density populations with self-compatible breeding systems; characteristics which the BFH would predict lead to high local genetic differentiation. We test this prediction for five Piper species on Barro Colorado Island, Panama, using Amplified Fragment Length Polymorphism (AFLP) markers. All species showed strong genetic structure at both fine- and large-spatial scales. Over short distances (200–750 m) populations showed significant genetic differentiation (Fst 0.11–0.46, P < 0.05), with values of spatial genetic structure that exceed those reported for other tropical tree species (Sp = 0.03–0.136). This genetic structure probably results from the combined effects of limited seed and pollen dispersal, clonal spread, and selfing. These processes are likely to have facilitated the diversification of populations in response to local natural selection or genetic drift and may explain the remarkable diversity of this rich genus. PMID:22393518

Automatic differentiation algorithms in model analysis

NARCIS (Netherlands)

Huiskes, M.J.

2002-01-01

<strong>Title:> Automatic differentiation algorithms in model analysis
<strong>Author:> M.J. Huiskes
<strong>Date:> 19 March, 2002

In this thesis automatic differentiation algorithms and derivative-based methods

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

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly manag...

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

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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

Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations.

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Badro, Danielle A; Douaihy, Bouchra; Haber, Marc; Youhanna, Sonia C; Salloum, Angélique; Ghassibe-Sabbagh, Michella; Johnsrud, Brian; Khazen, Georges; Matisoo-Smith, Elizabeth; Soria-Hernanz, David F; Wells, R Spencer; Tyler-Smith, Chris; Platt, Daniel E; Zalloua, Pierre A

2013-01-01

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of F(ST)'s, R(ST)'s, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Differential influences of local subpopulations on regional diversity and differentiation for greater sage-grouse (Centrocercus urophasianus)

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Row, Jeffery R.; Oyler-McCance, Sara J.; Fedy, Brad C.

2016-01-01

The distribution of spatial genetic variation across a region can shape evolutionary dynamics and impact population persistence. Local population dynamics and among-population dispersal rates are strong drivers of this spatial genetic variation, yet for many species we lack a clear understanding of how these population processes interact in space to shape within-species genetic variation. Here, we used extensive genetic and demographic data from 10 subpopulations of greater sage-grouse to parameterize a simulated approximate Bayesian computation (ABC) model and (i) test for regional differences in population density and dispersal rates for greater sage-grouse subpopulations in Wyoming, and (ii) quantify how these differences impact subpopulation regional influence on genetic variation. We found a close match between observed and simulated data under our parameterized model and strong variation in density and dispersal rates across Wyoming. Sensitivity analyses suggested that changes in dispersal (via landscape resistance) had a greater influence on regional differentiation, whereas changes in density had a greater influence on mean diversity across all subpopulations. Local subpopulations, however, varied in their regional influence on genetic variation. Decreases in the size and dispersal rates of central populations with low overall and net immigration (i.e. population sources) had the greatest negative impact on genetic variation. Overall, our results provide insight into the interactions among demography, dispersal and genetic variation and highlight the potential of ABC to disentangle the complexity of regional population dynamics and project the genetic impact of changing conditions.

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.

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

Science.gov (United States)

Johnston, Lyza; Miller, Margaret W; Baums, Iliana B

2012-01-01

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.

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

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Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

2017-09-01

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population

Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region.

Science.gov (United States)

Zhang, Yi; Lu, Yongfang; Yindee, Marnoch; Li, Kuan-Yi; Kuo, Hsiao-Yun; Ju, Yu-Ten; Ye, Shaohui; Faruque, Md Omar; Li, Qiang; Wang, Yachun; Cuong, Vu Chi; Pham, Lan Doan; Bouahom, Bounthong; Yang, Bingzhuang; Liang, Xianwei; Cai, Zhihua; Vankan, Dianne; Manatchaiworakul, Wallaya; Kowlim, Nonglid; Duangchantrasiri, Somphot; Wajjwalku, Worawidh; Colenbrander, Ben; Zhang, Yuan; Beerli, Peter; Lenstra, Johannes A; Barker, J Stuart F

2016-04-01

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock. © 2015 John Wiley & Sons Ltd.

New microsatellites revealed strong gene flow among populations of a new outbreak pest, Athetis lepigone (Möschler).

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Zhu, W-C; Sun, J-T; Dai, J; Huang, J-R; Chen, L; Hong, X-Y

2017-11-27

Athetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.

Microallopatry caused strong diversification in Buthus scorpions (Scorpiones: Buthidae in the Atlas Mountains (NW Africa.

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Jan C Habel

Full Text Available The immense biodiversity of the Atlas Mountains in North Africa might be the result of high rates of microallopatry caused by mountain barriers surpassing 4000 meters leading to patchy habitat distributions. We test the influence of geographic structures on the phylogenetic patterns among Buthus scorpions using mtDNA sequences. We sampled 91 individuals of the genus Buthus from 51 locations scattered around the Atlas Mountains (Antiatlas, High Atlas, Middle Atlas and Jebel Sahro. We sequenced 452 bp of the Cytochrome Oxidase I gene which proved to be highly variable within and among Buthus species. Our phylogenetic analysis yielded 12 distinct genetic groups one of which comprised three subgroups mostly in accordance with the orographic structure of the mountain systems. Main clades overlap with each other, while subclades are distributed parapatrically. Geographic structures likely acted as long-term barriers among populations causing restriction of gene flow and allowing for strong genetic differentiation. Thus, genetic structure and geographical distribution of genetic (subclusters follow the classical theory of allopatric differentiation where distinct groups evolve without range overlap until reproductive isolation and ecological differentiation has built up. Philopatry and low dispersal ability of Buthus scorpions are the likely causes for the observed strong genetic differentiation at this small geographic scale.

Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers.

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Ahmed Mohamed, Nadjim; Yu, Qian; Chanfi, Mohamed Ibrahim; Li, Yangping; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

2016-01-01

Small giant clam, Tridacna maxima , widely distributed from French Polynesia to East Africa, has faced population declines due to over-exploitation. Comoros islands are an important biogeographic region due to potential richness of marine species, but no relevant information is available. In order to facilitate devising effective conservation management plan for T. maxima , nine microsatellite markers were used to survey genetic diversity and population differentiation of 72 specimens collected from three Comoros islands, Grande Comore, Moheli and Anjouan. A total of 51 alleles were detected ranged from 2 to 8 per locus. Observed and expected heterozygosity varied from 0.260 to 0.790 and from 0.542 to 0.830, respectively. All populations have high genetic diversity, especially the population in Moheli, a protected area, has higher genetic diversity than the others. Significant heterozygote deficiencies were recorded, and null alleles were probably the main factor leading to these deficits. F ST value indicated medium genetic differentiation among the populations. Although significant, AMOVA revealed 48.9 % of genetic variation within individuals and only a small variation of 8.9 % was found between populations. Gene flow was high ( Nm  = 12.40) between Grande Comore and Moheli, while lower ( Nm  = 1.80) between Grande Comore and Anjouan, explaining geographic barriers to genetic exchanges might exist in these two islands. Global gene flow analysis ( Nm  = 5.50) showed that larval dispersal is enough to move between the islands. The high genetic diversity and medium population differentiation revealed in the present study offer useful information on genetic conservation of small giant clams.

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

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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.

Ecotypic differentiation between urban and rural populations of the grasshopper Chorthippus brunneus relative to climate and habitat fragmentation.

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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.

Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection.

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Campo, D; Lehmann, K; Fjeldsted, C; Souaiaia, T; Kao, J; Nuzhdin, S V

2013-10-01

The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale. © 2013 John Wiley & Sons Ltd.

Coherent population trapping magnetometer by differential detecting magneto–optic rotation effect

International Nuclear Information System (INIS)

Zhang Fan; Tian Yuan; Zhang Yi; Gu Si-Hong

2016-01-01

A pocket coherent population trapping (CPT) atomic magnetometer scheme that uses a vertical cavity surface emitting laser as a light source is proposed and experimentally investigated. Using the differential detecting magneto–optic rotation effect, a CPT spectrum with the background canceled and a high signal-to-noise ratio is obtained. The experimental results reveal that the sensitivity of the proposed scheme can be improved by half an order, and the ability to detect weak magnetic fields is extended one-fold. Therefore, the proposed scheme is suited to realize a pocket-size CPT magnetometer. (paper)

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

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Macdonald, Virginia; Verster, Annette; Baggaley, Rachel

2017-07-21

Key populations (KPs) are disproportionally affected by HIV and have low rates of access to HIV testing and treatment services compared to the broader population. WHO promotes the use of differentiated approaches for reaching and recruiting KP into the HIV services continuum. These approaches may help increase access to KPs who are often criminalized or stigmatized. By catering to the specific needs of each KP individual, differentiated approaches may increase service acceptability, quality and coverage, reduce costs and support KP members in leading the HIV response among their communities. WHO recommends the implementation of community-based and lay provider administered HIV testing services. Together, these approaches reduce barriers and costs associated with other testing strategies, allow greater ownership in HIV programmes for KP members and reach more people than do facility-based services. Despite this evidence availability and support for them is limited. Peer-driven interventions have been shown to be effective in engaging, recruiting and supporting clients. Some programmes employ HIV-positive or non-PLHIV "peer navigators" and other staff to provide case management, enrolment and/or re-enrolment in care and treatment services. However, a better understanding of the impact, cost effectiveness and potential burden on peer volunteers is required. Task shifting and non-facility-based service locations for antiretroviral therapy (ART) initiation and maintenance and antiretroviral (ARV) distribution are recommended in both the consolidated HIV treatment and KP guidelines of WHO. These approaches are accepted in generalized epidemics and for the general population where successful models exist; however, few organizations provide or initiate ART at KP community-based services. 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

Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure.

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Orsini, Luisa; Marshall, Hollie; Cuenca Cambronero, Maria; Chaturvedi, Anurag; Thomas, Kelley W; Pfrender, Michael E; Spanier, Katina I; De Meester, Luc

2016-12-01

Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank. © 2016 John Wiley & Sons Ltd.

Differential contribution of demographic rate synchrony to population synchrony in barn swallows.

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Schaub, Michael; von Hirschheydt, Johann; Grüebler, Martin U

2015-11-01

Populations of many species show temporally synchronous dynamics over some range, mostly caused by spatial autocorrelation of the environment that affects demographic rates. Synchronous fluctuation of a demographic rate is a necessary, but not sufficient condition for population synchrony because population growth is differentially sensitive to variation in demographic rates. Little is known about the relative effects of demographic rates to population synchrony, because it is rare that all demographic rates from several populations are known. We develop a hierarchical integrated population model with which all relevant demographic rates from all study populations can be estimated and apply it to demographic data of barn swallows Hirundo rustica from nine sites that were between 19 and 224 km apart from each other. We decompose the variation of the population growth and of the demographic rates (apparent survival, components of productivity, immigration) into global and local temporal components using random effects which allowed the estimation of synchrony of these rates. The barn swallow populations fluctuated synchronously, but less so than most demographic rates. The highest synchrony showed the probability of double brooding, while fledging success was highly asynchronous. Apparent survival, immigration and total productivity achieved intermediate levels of synchrony. The growth of all populations was most sensitive to changes in immigration and adult apparent survival, and both of them contributed to the observed temporal variation of population growth rates. Using a simulation model, we show that immigration and apparent survival of juveniles and adults were able to induce population synchrony, but not components of local productivity due to their low population growth rate sensitivity. Immigrants are mostly first-time breeders, and consequently, their number depends on the productivity of neighbouring populations. Since total productivity was synchronized

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.

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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.

Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species.

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Tschirren, Barbara; Andersson, Martin; Scherman, Kristin; Westerdahl, Helena; Råberg, Lars

2012-03-01

Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defense may be evolutionarily more dynamic than has previously been appreciated. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Differential Evolution Algorithm with Self-Adaptive Population Resizing Mechanism

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Xu Wang

2013-01-01

Full Text Available A differential evolution (DE algorithm with self-adaptive population resizing mechanism, SapsDE, is proposed to enhance the performance of DE by dynamically choosing one of two mutation strategies and tuning control parameters in a self-adaptive manner. More specifically, more appropriate mutation strategies along with its parameter settings can be determined adaptively according to the previous status at different stages of the evolution process. To verify the performance of SapsDE, 17 benchmark functions with a wide range of dimensions, and diverse complexities are used. Nonparametric statistical procedures were performed for multiple comparisons between the proposed algorithm and five well-known DE variants from the literature. Simulation results show that SapsDE is effective and efficient. It also exhibits much more superiorresultsthan the other five algorithms employed in the comparison in most of the cases.

Colonization of a territory by a stochastic population under a strong Allee effect and a low immigration pressure

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Be'er, Shay; Assaf, Michael; Meerson, Baruch

2015-06-01

We study the dynamics of colonization of a territory by a stochastic population at low immigration pressure. We assume a sufficiently strong Allee effect that introduces, in deterministic theory, a large critical population size for colonization. At low immigration rates, the average precolonization population size is small, thus invalidating the WKB approximation to the master equation. We circumvent this difficulty by deriving an exact zero-flux solution of the master equation and matching it with an approximate nonzero-flux solution of the pertinent Fokker-Planck equation in a small region around the critical population size. This procedure provides an accurate evaluation of the quasistationary probability distribution of population sizes in the precolonization state and of the mean time to colonization, for a wide range of immigration rates. At sufficiently high immigration rates our results agree with WKB results obtained previously. At low immigration rates the results can be very different.

Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

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Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

2012-09-01

House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique.

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Bartáková, Veronika; Reichard, Martin; Janko, Karel; Polačik, Matej; Blažek, Radim; Reichwald, Kathrin; Cellerino, Alessandro; Bryja, Josef

2013-09-12

Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary

Analysis of cross-population differentiation between Thoroughbred and Jeju horses.

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Lee, Wonseok; Shin, Donghyn; Taye, Mengistie; Lee, Chul; Kim, Heebal; Lee, Hak-Kyo; Park, Kyung-Do

2017-12-19

This study was intended to identify genes positively selected in Thoroughbred horses (THBs) that potentially contribute to their running performances. The genomes of THB and Jeju horses (JH, Korean native horse) were compared to identify genes positively selected in THB. We performed cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio test (XP-CLR) statistical methods for our analysis using whole genome resequencing data of 14 THB and 6 JH. We identified 98 (XP-EHH) and 200 (XP-CLR) genes that are under positive selection in THB. Gene enrichment analysis identified 72 BP terms. The genes and BP terms explained some of THB's characteristics such as immunity, energy metabolism and eye size and function related to running performances. GO terms that play key roles in several cell signaling mechanisms, which affected ocular size and visual functions were identified. GO term Eye photoreceptor cell differentiation is among the terms annotated presumed to affect eye size. Our analysis revealed some positively selected candidate genes in THB related to their racing performances. The genes detected are related to the immunity, ocular size and function, and energy metabolism.

Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms.

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Bahri, Raoudha; El Moncer, Wifak; Al-Batayneh, Khalid; Sadiq, May; Esteban, Esther; Moral, Pedro; Chaabani, Hassen

2012-05-01

Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.

Elevation, Not Deforestation, Promotes Genetic Differentiation in a Pioneer Tropical Tree.

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Castilla, Antonio R; Pope, Nathaniel; Jaffé, Rodolfo; Jha, Shalene

2016-01-01

The regeneration of disturbed forest is an essential part of tropical forest ecology, both with respect to natural disturbance regimes and large-scale human-mediated logging, grazing, and agriculture. Pioneer tree species are critical for facilitating the transition from deforested land to secondary forest because they stabilize terrain and enhance connectivity between forest fragments by increasing matrix permeability and initiating disperser community assembly. Despite the ecological importance of early successional species, little is known about their ability to maintain gene flow across deforested landscapes. Utilizing highly polymorphic microsatellite markers, we examined patterns of genetic diversity and differentiation for the pioneer understory tree Miconia affinis across the Isthmus of Panama. Furthermore, we investigated the impact of geographic distance, forest cover, and elevation on genetic differentiation among populations using circuit theory and regression modeling within a landscape genetics framework. We report marked differences in historical and contemporary migration rates and moderately high levels of genetic differentiation in M. affinis populations across the Isthmus of Panama. Genetic differentiation increased significantly with elevation and geographic distance among populations; however, we did not find that forest cover enhanced or reduced genetic differentiation in the study region. Overall, our results reveal strong dispersal for M. affinis across human-altered landscapes, highlighting the potential use of this species for reforestation in tropical regions. Additionally, this study demonstrates the importance of considering topography when designing programs aimed at conserving genetic diversity within degraded tropical landscapes.

Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

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Arnett Donna

2009-08-01

Full Text Available Abstract Background Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years and compared them to similarly aged non-Hispanic whites (NHW (n = 597. Results Minor allele frequency (MAF distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusion These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans.

Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China.

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Zhao, Wei; Shi, Xiaozheng; Li, Jiangnan; Guo, Wei; Liu, Chengbai; Chen, Xia

2014-01-01

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = -0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

Patterns of genetic diversity and differentiation in the tsetse fly Glossina morsitans morsitans Westwood populations in East and southern Africa

International Nuclear Information System (INIS)

Ouma, J.O.; Marquez, J.G.; Krafsur, E.S

2007-01-01

Genetic diversity and differentiation within and among nine G. morsitans morsitans populations from East and southern Africa was assessed by examining variation at seven microsatellite loci and a mitochondrial locus, cytochrome oxidase (COI). Mean COI diversity within populations was 0.63 ± 0.33 and 0.81 taken over all populations. Diversities averaged over microsatellite loci were high (mean number of alleles/locus ≥7.4; mean HE ≥ 65%) in all populations. Diversities averaged across populations were greater in East Africa (mean number of alleles = 22 ± 2.6; mean he = 0.773 ± 0.033) than in southern Africa (mean number of alleles = 18.7 ± 4.0; mean he = 0.713 ± 0.072). Differentiation among all populations was highly significant (RST = 0.25, FST = 0.132). Nei’s Gij statistics were 0.09 and 0.19 within regions for microsatellites and mitochondria, respectively; between regions, Gij was 0.14 for microsatellites and 0.23 for mitochondria. GST among populations was 0.23 for microsatellite loci and 0.40 for mitochondria. The F, G and R statistics indicate highly restricted gene flow among G. m. morsitans populations separated over geographic scales of 12–917 km. (author)

High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus).

Science.gov (United States)

Defaveri, Jacquelin; Shikano, Takahito; Shimada, Yukinori; Merilä, Juha

2013-09-01

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene-based genome-scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection-as determined with several outlier detection methods-was low (F(ST) = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (F(ST) = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes. © 2013 John Wiley & Sons Ltd.

Strong interactions

International Nuclear Information System (INIS)

Froissart, Marcel

1976-01-01

Strong interactions are introduced by their more obvious aspect: nuclear forces. In hadron family, the nucleon octet, OMEGA - decuplet, and quark triply are successively considered. Pion wave having been put at the origin of nuclear forces, low energy phenomena are described, the force being explained as an exchange of structure corresponding to a Regge trajectory in a variable rotating state instead of the exchange of a well defined particle. At high energies the concepts of pomeron, parton and stratons are introduced, pionization and fragmentation are briefly differentiated [fr

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.

Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China.

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Wei Zhao

Full Text Available Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR and methylation-sensitive amplified polymorphism (MSAP markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88% was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%. UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = -0.95 for HPLC fingerprint and altitude. Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

Female Choice Undermines the Emergence of Strong Sexual Isolation between Locally Adapted Populations of Atlantic Mollies (Poecilia mexicana

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Claudia Zimmer

2018-05-01

Full Text Available Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI. Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate choice component of prezygotic RI. Mate choice tests across drainages (with stimulus males from another drainage suggest that specific features of the males coupled with a general female preference for yellow color patterns explain the observed variation. Analyses of male body coloration identified the intensity of yellow fin coloration as a strong candidate to explain this pattern, and common-garden rearing suggested heritable population differences. Male sexual ornamentation apparently evolved differently across sulfide-adapted populations, for example because of differences in natural counterselection via predation. The ubiquitous preference for yellow color ornaments in poeciliid females likely undermines the emergence of strong RI, as female discrimination in favor of own males becomes weaker when yellow fin coloration in the respective sulfide ecotype increases. Our study illustrates the complexity of the (partly non-parallel pathways to divergence among replicated ecological gradients. We suggest that future work should identify the genomic loci involved in the pattern reported here, making use of the increasing genomic and transcriptomic datasets available for our study system.

Replicated population divergence caused by localized coevolution? A test of three hypotheses in the red crossbill-lodgepole pine system.

Science.gov (United States)

Edelaar, P; Benkman, C W

2006-09-01

Several lines of evidence support the hypothesis that local populations of red crossbills (Loxia curvirostra complex) enter into a predator-prey arms race with lodgepole pine (Pinus contorta latifolia) in the absence of competing pine squirrels (Tamiasciurus hudsonicus). Nevertheless, the alternative hypotheses that neutral evolution or factors other than squirrels have caused crossbill population differentiation have not been thoroughly tested. We compared crossbill and pine cone morphology between island populations where squirrels are absent or present, and mainland sites where squirrels are present, in order to distinguish among these hypotheses. All comparisons supported an effect of squirrel absence, not island status, on crossbill and cone morphology. Hence our results provide further evidence that strong localized coevolutionary interactions in a geographic mosaic have driven adaptive population differentiation. In addition, vocal differentiation of crossbills was related to the absence of squirrels, but not to island status. As morphological and vocal differentiation is correlated with reproductive isolation in crossbills, the geographic mosaic of coevolution also seems to promote ecological speciation.

Strong field coherent control of atomic population transfer

International Nuclear Information System (INIS)

Trallero-Herrero, Carlos; Clow, Stephen D; Bergeman, Thomas; Weinacht, Thomas

2008-01-01

We demonstrate a population inversion in a three-level system via three-photon absorption from a single shaped ultrafast laser pulse. The optimal pulse shape for the inversion is discovered using closed-loop learning control and interpreted via pulse shape parameter scans and numerical integration of the Schroedinger equation. The population inversion is measured using a combination of spontaneous and stimulated emissions. Our results illustrate the importance of dynamic Stark shifts in coherent multi-photon excitation

Genetic diversity and substantial population differentiation in Crassostrea hongkongensis revealed by mitochondrial DNA.

Science.gov (United States)

Li, Lu; Wu, Xiangyun; Yu, Ziniu

2013-09-01

The Hong Kong oyster, Crassostrea hongkongensis, is an important fisheries resource that is cultivated in the coastal waters of the South China Sea. Despite significant advances in understanding biological and taxonomic aspects of this species, no detailed study of its population genetic diversity in regions of extensive cultivation are available. Direct sequencing of the mtDNA cox1 gene region was used to investigate genetic variation within and between eleven C. hongkongensis populations collected from typical habitats. Sixty-two haplotypes were identified; only haplotype 2 (21.74% of total haplotypes) was shared among all the eleven populations, and most of the observed haplotypes were restricted to individual populations. Both AMOVA and FST analyses revealed significant population structure, and the isolation by distance (IBD) was confirmed. The highest local differentiation was observed between the sample pools from Guangxi versus Guangdong and Fujian, which are separated by a geographic barrier, the Leizhou Peninsula. Current knowledge from seed management suggests that seed transfer from Guangxi province has likely reduced the divergence that somewhat naturally exists between these pools. The findings from the present study could be useful for genetic management and may serve as a baseline by which to monitor future changes in genetic diversity, either due to natural or anthropogenic impacts. Copyright © 2013 Elsevier B.V. All rights reserved.

Genomic differentiation and demographic histories of Atlantic and Indo-Pacific yellowfin tuna (Thunnus albacares) populations.

Science.gov (United States)

Barth, J M I; Damerau, M; Matschiner, M; Jentoft, S; Hanel, R

2017-04-13

Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

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John S K Kauwe

Full Text Available Alzheimer's disease (AD is an international health concern that has a devastating effect on patients and families. While several genetic risk factors for AD have been identified much of the genetic variance in AD remains unexplained. There are limited published assessments of the familiality of Alzheimer's disease. Here we present the largest genealogy-based analysis of AD to date.We assessed the familiality of AD in The Utah Population Database (UPDB, a population-based resource linking electronic health data repositories for the state with the computerized genealogy of the Utah settlers and their descendants. We searched UPDB for significant familial clustering of AD to evaluate the genetic contribution to disease. We compared the Genealogical Index of Familiality (GIF between AD individuals and randomly selected controls and estimated the Relative Risk (RR for a range of family relationships. Finally, we identified pedigrees with a significant excess of AD deaths.The GIF analysis showed that pairs of individuals dying from AD were significantly more related than expected. This excess of relatedness was observed for both close and distant relationships. RRs for death from AD among relatives of individuals dying from AD were significantly increased for both close and more distant relatives. Multiple pedigrees had a significant excess of AD deaths.These data strongly support a genetic contribution to the observed clustering of individuals dying from AD. This report is the first large population-based assessment of the familiality of AD mortality and provides the only reported estimates of relative risk of AD mortality in extended relatives to date. The high-risk pedigrees identified show a true excess of AD mortality (not just multiple cases and are greater in depth and width than published AD pedigrees. The presence of these high-risk pedigrees strongly supports the possibility of rare predisposition variants not yet identified.

Genetic differentiation in Pyrenophora teres f. teres populations from Syria and Tunisia as assessed by AFLP markers.

Science.gov (United States)

Bouajila, A; Zoghlami, N; Murad, S; Baum, M; Ghorbel, A; Nazari, K

2013-06-01

To investigate the level of genetic differentiation and diversity among Pyrenophora teres isolate populations originating from different agro-ecological areas of Syria and Tunisia and to determine the potential of AFLP profiling in genotyping Pyrenophora teres f. teres. In this study, AFLP markers have been employed to identify patterns of population structure in 20 Pyrenophora teres f. teres populations from Syria and Tunisia. Ninety-four isolates were studied by the use of a protocol that involved stringent PCR amplification of fragments derived from digestion of genomic DNA with restriction enzymes EcoRI and MesI. Based on 401 amplified polymorphic DNA markers (AFLP), variance analyses indicated that most of the variation was partitioned within rather than between populations. Genotypic diversity (GD) was high for populations from Rihane, local landraces and different agro-ecological zones (GD = 0·75-0·86). There was high genetic differentiation among pathogen populations from different host populations in Syria (Gst  = 0·31, ht = 0·190) and Tunisia (Gst  = 0·39, ht = 0·263), which may be partly explained by the low gene flow around the areas sampled. A phenetic tree revealed three groups with high bootstrap values (55, 68, 76) and reflected the grouping of isolates based on host, or agro-ecological areas. AFLP profiling is an effective method for typing the genetically diverse pathogen Pyrenophora teres f. teres. The study represents a comparative analysis of the genetic diversity in P. teres isolates from two countries spanning two continents and also shows that several distinct P. teres genotypes may be found in a given environment. The implications of these findings for Pyrenophora teres f. teres evolutionary potential and net blotch-resistance breeding in Syria and Tunisia were also discussed. © 2012 The Society for Applied Microbiology.

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

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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.

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.

Population differentiation of the shore crab Carcinus maenas (Brachyura: Portunidae on the southwest English coast based on genetic and morphometric analyses

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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.

Habitat differentiation vs. isolation-by-distance : the genetic population structure of Elymus athericus in European salt marshes

NARCIS (Netherlands)

Bockelmann, AC; Reusch, TBH; Bijlsma, R; Bakker, JP

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt-marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the

Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks.

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Mark Ravinet

Full Text Available Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L. forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12, we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an

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...... harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull...

Homogenization techniques for population dynamics in strongly heterogeneous landscapes.

Science.gov (United States)

Yurk, Brian P; Cobbold, Christina A

2018-12-01

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction-diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.

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

KAUST Repository

Montes, Iratxe; Zarraonaindia, Iratxe; Iriondo, Mikel; Grant, W. Stewart; Manzano, Carmen; Cotano, Unai; Conklin, Darrell; Irigoien, Xabier; Estonba, Andone

2016-01-01

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

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

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

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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.

The Population Structure of Phytophthora infestans from the Toluca Valley of Central Mexico Suggests Genetic Differentiation Between Populations from Cultivated Potato and Wild Solanum spp.

Science.gov (United States)

Flier, Wilbert G; Grünwald, Niklaus J; Kroon, Laurens P N M; Sturbaum, Anne K; van den Bosch, Trudy B M; Garay-Serrano, Edith; Lozoya-Saldaña, Hector; Fry, William E; Turkensteen, Lod J

2003-04-01

ABSTRACT The population structure of Phytophthora infestans in the Toluca Valley of central Mexico was assessed using 170 isolates collected from cultivated potatoes and the native wild Solanum spp., S. demissum and S. xendinense. All isolates were analyzed for mitochondrial DNA (mtDNA) haplotype and amplified fragment length polymorphism (AFLP) multi-locus fingerprint genotype. Isolate samples were monomorphic for mtDNA haplotype because all isolates tested were of the Ia haplotype. A total of 158 multilocus AFLP genotypes were identified among the 170 P. infestans isolates included in this study. P. infestans populations sampled in the Toluca Valley in 1997 were highly variable and almost every single isolate represented a unique genotype based on the analysis of 165 AFLP marker loci. Populations of P. infestans collected from the commercial potato-growing region in the valley, the subsistence potato production area along the slopes of the Nevado de Toluca, and the native Solanum spp. on the forested slopes of the volcano showed a high degree of genetic diversity. The number of polymorphic loci varied from 20.0 to 62.4% for isolates collected from the field station and wild Solanum spp. On average, 81.8% (135) of the AFLP loci were polymorphic. Hetero-zygosity varied between 7.7 and 19.4%. Significant differentiation was found at the population level between strains originating from cultivated potatoes and wild Solanum spp. (P = 0.001 to 0.022). Private alleles were observed in individual isolates collected from all three populations, with numbers of unique dominant alleles varying from 9 to 16 for isolates collected from commercial potato crops and native Solanum spp., respectively. Four AFLP markers were exclusively found present in isolates collected from S. demissum. Indirect estimation of gene flow between populations indicated restricted gene flow between both P. infestans populations from cultivated potatoes and wild Solanum hosts. There was no evidence

Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar.

Science.gov (United States)

Perry, George H; Louis, Edward E; Ratan, Aakrosh; Bedoya-Reina, Oscar C; Burhans, Richard C; Lei, Runhua; Johnson, Steig E; Schuster, Stephan C; Miller, Webb

2013-04-09

We performed a population genomics study of the aye-aye, a highly specialized nocturnal lemur from Madagascar. Aye-ayes have low population densities and extensive range requirements that could make this flagship species particularly susceptible to extinction. Therefore, knowledge of genetic diversity and differentiation among aye-aye populations is critical for conservation planning. Such information may also advance our general understanding of Malagasy biogeography, as aye-ayes have the largest species distribution of any lemur. We generated and analyzed whole-genome sequence data for 12 aye-ayes from three regions of Madagascar (North, West, and East). We found that the North population is genetically distinct, with strong differentiation from other aye-ayes over relatively short geographic distances. For comparison, the average FST value between the North and East aye-aye populations--separated by only 248 km--is over 2.1-times greater than that observed between human Africans and Europeans. This finding is consistent with prior watershed- and climate-based hypotheses of a center of endemism in northern Madagascar. Taken together, these results suggest a strong and long-term biogeographical barrier to gene flow. Thus, the specific attention that should be directed toward preserving large, contiguous aye-aye habitats in northern Madagascar may also benefit the conservation of other distinct taxonomic units. To help facilitate future ecological- and conservation-motivated population genomic analyses by noncomputational biologists, the analytical toolkit used in this study is available on the Galaxy Web site.

Sex-differentiated migration patterns, protandry and phenology in North European songbird populations

DEFF Research Database (Denmark)

Tøttrup, Anders Peter; Thorup, Kasper

2008-01-01

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....

The Limited Utility of Multiunit Data in Differentiating Neuronal Population Activity.

Directory of Open Access Journals (Sweden)

Corey J Keller

Full Text Available To date, single neuron recordings remain the gold standard for monitoring the activity of neuronal populations. Since obtaining single neuron recordings is not always possible, high frequency or 'multiunit activity' (MUA is often used as a surrogate. Although MUA recordings allow one to monitor the activity of a large number of neurons, they do not allow identification of specific neuronal subtypes, the knowledge of which is often critical for understanding electrophysiological processes. Here, we explored whether prior knowledge of the single unit waveform of specific neuron types is sufficient to permit the use of MUA to monitor and distinguish differential activity of individual neuron types. We used an experimental and modeling approach to determine if components of the MUA can monitor medium spiny neurons (MSNs and fast-spiking interneurons (FSIs in the mouse dorsal striatum. We demonstrate that when well-isolated spikes are recorded, the MUA at frequencies greater than 100Hz is correlated with single unit spiking, highly dependent on the waveform of each neuron type, and accurately reflects the timing and spectral signature of each neuron. However, in the absence of well-isolated spikes (the norm in most MUA recordings, the MUA did not typically contain sufficient information to permit accurate prediction of the respective population activity of MSNs and FSIs. Thus, even under ideal conditions for the MUA to reliably predict the moment-to-moment activity of specific local neuronal ensembles, knowledge of the spike waveform of the underlying neuronal populations is necessary, but not sufficient.

On the strong solution of a class of partial differential equations that arise in the pricing of mortgage backed securities

KAUST Repository

Parshad, Rana; Bayazit, Derviş; Barlow, Nathaniel S.; Prasad, V. Ramchandra

2011-01-01

We consider a reduced form pricing model for mortgage backed securities, formulated as a non-linear partial differential equation. We prove that the model possesses a weak solution. We then show that under additional regularity assumptions on the initial data, we also have a mild solution. This mild solution is shown to be a strong solution via further regularity arguments. We also numerically solve the reduced model via a Fourier spectral method. Lastly, we compare our numerical solution to real market data. We observe interestingly that the reduced model captures a number of recent market trends in this data, that have escaped previous models.

Intervention strength does not differentially affect memory reconsolidation of strong memories.

Science.gov (United States)

van Schie, Kevin; van Veen, Suzanne C; Hendriks, Yanniek R; van den Hout, Marcel A; Engelhard, Iris M

2017-10-01

Recently, it has become clear that retrieval (i.e., reactivation) of consolidated memories may return these memories into a labile state before they are restored into long-term memory ('reconsolidation'). Using behavioral manipulations, reactivated memories can be disrupted via the mechanism of novel learning. In the present study, we investigated whether changing a strong memory during reconsolidation depends on the strength of novel learning. To test this, participants (N=144) in six groups acquired a relatively strong memory on Day 1 by viewing and recalling a series of pictures three times. On Day 8, these pictures were reactivated in three groups, and they were not reactivated in the other three groups. Then, participants viewed and recalled new pictures once (weak new learning) or three times (strong new learning), or they did not learn any new pictures. On Day 9, participants performed a recognition test in which their memory for Day 1 pictures was assessed. Two main results are noted. First, the groups that reactivated pictures from Day 1 and received weak or strong new learning did not differ in memory performance. Second, these two groups consistently performed similar to groups that controlled for new learning without reactivation. Because these results contradict what was expected based on the reconsolidation hypothesis, we discuss possible explanations and implications. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

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Yun Duan

Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

Genetic structure and demographic history of brown trout ( Salmo trutta ) populations from the southern Balkans

DEFF Research Database (Denmark)

Apostolidis, A.P.; Madeira, M.J.; Hansen, Michael Møller

2008-01-01

1. The present study was designed to characterize the genetic structure of brown trout (Salmo trutta) populations from the southern Balkans and to assess the spread of non-native strains and their introgression into native trout gene pools. We analysed polymorphism at nine microsatellite loci...... in seven supposedly non-admixed and three stocked brown trout populations. 2. The analyses confirmed the absence of immigration and extraordinarily strong genetic differentiation among the seven non-introgressed populations in parallel with low levels of intrapopulation genetic variability. In contrast...

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].

Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy.

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Ilin, Yelena; Choi, Ji Sun; Harley, Brendan A C; Kraft, Mary L

2015-11-17

A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that

Probabilistic models of population evolution scaling limits, genealogies and interactions

CERN Document Server

Pardoux, Étienne

2016-01-01

This expository book presents the mathematical description of evolutionary models of populations subject to interactions (e.g. competition) within the population. The author includes both models of finite populations, and limiting models as the size of the population tends to infinity. The size of the population is described as a random function of time and of the initial population (the ancestors at time 0). The genealogical tree of such a population is given. Most models imply that the population is bound to go extinct in finite time. It is explained when the interaction is strong enough so that the extinction time remains finite, when the ancestral population at time 0 goes to infinity. The material could be used for teaching stochastic processes, together with their applications. Étienne Pardoux is Professor at Aix-Marseille University, working in the field of Stochastic Analysis, stochastic partial differential equations, and probabilistic models in evolutionary biology and population genetics. He obtai...

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

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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) geothermal gradient in Yellowstone.

Sex-chromosome differentiation parallels postglacial range expansion in European tree frogs (Hyla arborea).

Science.gov (United States)

Dufresnes, Christophe; Bertholet, Youna; Wassef, Jérôme; Ghali, Karim; Savary, Romain; Pasteur, Baptiste; Brelsford, Alan; Rozenblut-Kościsty, Beata; Ogielska, Maria; Stöck, Matthias; Perrin, Nicolas

2014-12-01

Occasional XY recombination is a proposed explanation for the sex-chromosome homomorphy in European tree frogs. Numerous laboratory crosses, however, failed to detect any event of male recombination, and a detailed survey of NW-European Hyla arborea populations identified male-specific alleles at sex-linked loci, pointing to the absence of XY recombination in their recent history. Here, we address this paradox in a phylogeographic framework by genotyping sex-linked microsatellite markers in populations and sibships from the entire species range. Contrasting with postglacial populations of NW Europe, which display complete absence of XY recombination and strong sex-chromosome differentiation, refugial populations of the southern Balkans and Adriatic coast show limited XY recombination and large overlaps in allele frequencies. Geographically and historically intermediate populations of the Pannonian Basin show intermediate patterns of XY differentiation. Even in populations where X and Y occasionally recombine, the genetic diversity of Y haplotypes is reduced below the levels expected from the fourfold drop in copy numbers. This study is the first in which X and Y haplotypes could be phased over the distribution range in a species with homomorphic sex chromosomes; it shows that XY-recombination patterns may differ strikingly between conspecific populations, and that recombination arrest may evolve rapidly (<5000 generations). © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

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.

Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China.

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Fan, Liqiang; Zheng, Honglei; Milne, Richard I; Zhang, Lei; Mao, Kangshan

2018-03-14

Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species. Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG). Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during

A survey of Strong Convergent Schemes for the Simulation of ...

African Journals Online (AJOL)

We considered strong convergent stochastic schemes for the simulation of stochastic differential equations. The stochastic Taylor's expansion, which is the main tool used for the derivation of strong convergent schemes; the Euler Maruyama, Milstein scheme, stochastic multistep schemes, Implicit and Explicit schemes were ...

"MONOCLONAL ANTIBODY HBME-1 USEFULNESS IN DIFFERENTIATION OF BENIGN NEOPLASM AND DIFFERENTIATED THYROID CARCINOMA"

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M. Mokhtari

2005-05-01

Full Text Available HBME-l is an antimesothelial monoclonal antibody that recognizes an unknown antigen on microvilli of mesothelial cells. The antibody is only relatively specific for mesothelium and is used in the differential diagnosis of mesothelioma and adenocarcinoma within the context of an appropriate immuno-histochemical panel. HBME-l has also been reported to strongly and uniformly stain papillary and follicular carcinoma of the thyroid while benign disorders have been usually negative. We studied the immunoreactivity of HBME-l in 90 cases of benign and malignant thyroid lesions. We found strong positive staining in the majority of papillary carcinomas (28/31, in some of follicular carcinomas (4/6,and in a few follicular adenomas (2/17. Negative staining was found in oxyphilic cell adenoma (0/4, nodular goiter (0/13 and undifferentiated carcinoma. The results suggest that monoclonal antibody HBME-l is useful in differentiating papillary and follicular carcinoma of the thyroid from benign lesions, especially in more differentiated lesions. Strong and generalized immunoreactivity for HBME-l in a follicular lesion should raise the suspicion of malignancy, but negative staining specially in poorly differentiated lesion does not rule out malignancy.

Lack of Ecotypic Differentiation: Plant Response to Elevation, Population Origin, and Wind in the Luquillo Mountains, Puerto Rico

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Ned Fetcher; Roberto A. Cordero; Janice Voltzow

2000-01-01

How important is ecotypic differentiation along elevational gradients in the tropics? Reciprocal transplants of two shrubs, Clibadium erosum (Asteraceae) and Psychotria berteriana (Rubiaceae), and a palm, Prestoea acuminata var. montana (Palmaceae), were used to test for the effect of environment and population origin on growth and physiology in the Luquillo...

Molecular and behavioral differentiation among Brazilian populations of Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae).

Science.gov (United States)

Araki, Alejandra S; Vigoder, Felipe M; Bauzer, Luiz G S R; Ferreira, Gabriel E M; Souza, Nataly A; Araújo, Izeneide B; Hamilton, James G C; Brazil, Reginaldo P; Peixoto, Alexandre A

2009-01-01

Lutzomyia longipalpis is the primary vector of American visceral leishmaniasis. There is strong evidence that L. longipalpis is a species complex, but until recently the existence of sibling species among Brazilian populations was considered a controversial issue. In addition, there is still no consensus regarding the number of species occurring in this complex. Using period, a gene that controls circadian rhythms and affects interpulse interval periodicity of the male courtship songs in Drosophila melanogaster and close relatives, we analyzed the molecular polymorphism in a number of L. longipalpis samples from different regions in Brazil and compared the results with our previously published data using the same marker. We also studied the male copulation songs and pheromones from some of these populations. The results obtained so far suggest the existence of two main groups of populations in Brazil, one group representing a single species with males producing Burst-type copulation songs and cembrene-1 pheromones; and a second group that is more heterogeneous and probably represents a number of incipient species producing different combinations of Pulse-type songs and pheromones. Our results reveal a high level of complexity in the divergence and gene-flow among Brazilian populations of the L. longipalpis species complex. This raises important questions concerning the epidemiological consequences of this incipient speciation process.

Genetic differentiation in the populations of red piranha, Pygocentrus nattereri Kner (1860 (Characiformes: Serrasalminae, from the river basins of northeastern Brazil

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L. A. Luz

Full Text Available Abstract The red piranha, Pygocentrus nattereri, is an important resource for artisanal and commercial fisheries. The present study determines the genetic differentiation among P. nattereri populations from the northeastern Brazilian state of Maranhão. The DNA was isolated using a standard phenol-chloroform protocol and the Control Region was amplified by PCR. The PCR products were sequenced using the didesoxyterminal method. A sequence of 1039 bps was obtained from the Control Region of 60 specimens, which presented 33 polymorphic sites, 41 haplotypes, һ =0.978 and π =0.009. The neutrality tests (D and Fs were significant (P < 0.05 for most of the populations analyzed. The AMOVA indicated that most of the molecular variation (72% arises between groups. The fixation index was highly significant (FST = 0.707, P < 0.00001. The phylogenetic analyses indicated that the specimens represented a monophyletic group. Genetic distances between populations varied from 0.8% to 1.9%, and were <0.5% within populations. The degree of genetic differentiation found among the stocks of P. nattereri indicates the need for the development of independent management plans for the different river basins in order to preserve the genetic variability of their populations.

Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae dengue vector from the Brazilian state of Maranhão

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Andrelina Alves de Sousa

Full Text Available ABSTRACT Aedes (Stegomyia aegypti is the vector responsible for the transmission of the viruses that cause zika, yellow and chikungunya fevers, the four dengue fever serotypes (DENV - 1, 2, 3, 4, and hemorrhagic dengue fever in tropical and subtropical regions around the world. The present study investigated the genetic differentiation of the 15 populations of this vector in the Brazilian state of Maranhão, based on the mitochondrial ND4 marker. A total of 177 sequences were obtained for Aedes aegypti, with a fragment of 337 bps, 15 haplotypes, 15 polymorphics sites, haplotype diversity of h = 0.6938, and nucleotide diversity of π = 0.01486. The neutrality tests (D and Fs were not significant. The AMOVA revealed that most of the variation (58.47% was found within populations, with FST = 0.41533 (p < 0.05. Possible isolation by distance was tested and a significant correlation coefficient (r = 0.3486; p = 0.0040 was found using the Mantel test. The phylogenetic relationships among the 15 haplotypes indicated the existence of two distinct clades. This finding, together with the population parameters, was consistent with a pattern of genetic structuring that underpinned the genetic differentiation of the study populations in Maranhão, and was characterized by the presence of distinct lineages of Aedes aegypti.

AFLP genome scanning reveals divergent selection in natural populations of Liriodendron chinense (Magnoliaceae along a latitudinal transect

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Aihong eYang

2016-05-01

Full Text Available Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined AFLP genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Two complementary methods (Dfdist and BayeScan and association analysis between AFLP loci and climate factors were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity towards the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.

The genetic network controlling plasma cell differentiation.

Science.gov (United States)

Nutt, Stephen L; Taubenheim, Nadine; Hasbold, Jhagvaral; Corcoran, Lynn M; Hodgkin, Philip D

2011-10-01

Upon activation by antigen, mature B cells undergo immunoglobulin class switch recombination and differentiate into antibody-secreting plasma cells, the endpoint of the B cell developmental lineage. Careful quantitation of these processes, which are stochastic, independent and strongly linked to the division history of the cell, has revealed that populations of B cells behave in a highly predictable manner. Considerable progress has also been made in the last few years in understanding the gene regulatory network that controls the B cell to plasma cell transition. The mutually exclusive transcriptomes of B cells and plasma cells are maintained by the antagonistic influences of two groups of transcription factors, those that maintain the B cell program, including Pax5, Bach2 and Bcl6, and those that promote and facilitate plasma cell differentiation, notably Irf4, Blimp1 and Xbp1. In this review, we discuss progress in the definition of both the transcriptional and cellular events occurring during late B cell differentiation, as integrating these two approaches is crucial to defining a regulatory network that faithfully reflects the stochastic features and complexity of the humoral immune response. 2011 Elsevier Ltd. All rights reserved.

Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea.

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Postaire, Bautisse; Gélin, Pauline; Bruggemann, J Henrich; Pratlong, Marine; Magalon, Hélène

2017-10-01

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α ( sensu Postaire et al ., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive F IS values (from -0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (11,000 km distance), with significant pairwise F ST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.

Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

DEFF Research Database (Denmark)

Mucci, Nadia; Arrendal, Johanna; Ansorge, Hermann

2010-01-01

Eurasian otter populations strongly declined and partially disappeared due to global and local causes (habitat destruction, water pollution, human persecution) in parts of their continental range. Conservation strategies, based on reintroduction projects or restoration of dispersal corridors...... and landscape genetic analyses however indicate that local populations are genetically differentiated, perhaps as consequence of post-glacial demographic fluctuations and recent isolation. These results delineate a framework that should be used for implementing conservation programs in Europe, particularly...

Substructure of a Tunisian Berber population as inferred from 15 autosomal short tandem repeat loci.

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Khodjet-El-Khil, Houssein; Fadhlaoui-Zid, Karima; Gusmão, Leonor; Alves, Cíntia; Benammar-Elgaaied, Amel; Amorim, Antonio

2008-08-01

Currently, language and cultural practices are the only criteria to distinguish between Berber autochthonous Tunisian populations. To evaluate these populations' possible genetic structure and differentiation, we have analyzed 15 autosomal short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, and D19S433) in three southern Tunisian Berber groups: Sened, Matmata, and Chenini-Douiret. The exact test of population differentiation based on allele frequencies at the 15 loci shows significant P values at 7 loci between Chenini-Douiret and both Sened and Matmata, whereas just 5 loci show significant P values between Sened and Matmata. Comparative analyses between the three Berber groups based on genetic distances show that P values for F(ST) distances are significant between the three Berber groups. Population analysis performed using Structure shows a clear differentiation between these Berber groups, with strong genetic isolation of Chenini-Douiret. These results confirm at the autosomal level the high degree of heterogeneity of Tunisian Berber populations that had been previously reported for uniparental markers.

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

Science.gov (United States)

Gautier, Mathieu

2015-12-01

In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier

Uniform Selection as a Primary Force Reducing Population Genetic Differentiation of Cavitation Resistance across a Species Range

Science.gov (United States)

Lamy, Jean-Baptiste; Bouffier, Laurent; Burlett, Régis; Plomion, Christophe; Cochard, Hervé; Delzon, Sylvain

2011-01-01

Background Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. Methodology We assessed cavitation resistance (P 50), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F ST) and quantitative genetic differentiation (Q ST), for retrospective identification of the evolutionary forces acting on these traits. Results/Discussion In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h2 ns = 0.43±0.18, CVA = 4.4%). Q ST was significantly lower than F ST, indicating uniform selection for P 50, rather than genetic drift. Putative mechanisms underlying QST

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

Science.gov (United States)

Arunkumar, Ganeshprasad; Soria-Hernanz, David F; Kavitha, Valampuri John; Arun, Varatharajan Santhakumari; Syama, Adhikarla; Ashokan, Kumaran Samy; Gandhirajan, Kavandanpatti Thangaraj; Vijayakumar, Koothapuli; Narayanan, Muthuswamy; Jayalakshmi, Mariakuttikan; Ziegle, Janet S; Royyuru, Ajay K; Parida, Laxmi; Wells, R Spencer; Renfrew, Colin; Schurr, Theodore G; Smith, Chris Tyler; Platt, Daniel E; Pitchappan, Ramasamy

2012-01-01

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 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.

Population-Level Differentiation in Growth Rates and Leaf Traits in Seedlings of the Neotropical Live Oak Quercus oleoides Grown under Natural and Manipulated Precipitation Regimes

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Jose A. Ramírez-Valiente

2017-05-01

Full Text Available Widely distributed species are normally subjected to spatial heterogeneity in environmental conditions. In sessile organisms like plants, adaptive evolution and phenotypic plasticity of key functional traits are the main mechanisms through which species can respond to environmental heterogeneity and climate change. While extended research has been carried out in temperate species in this regard, there is still limited knowledge as to how species from seasonally-dry tropical climates respond to spatial and temporal variation in environmental conditions. In fact, studies of intraspecific genetically-based differences in functional traits are still largely unknown and studies in these ecosystems have largely focused on in situ comparisons where environmental and genetic effects cannot be differentiated. In this study, we tested for ecotypic differentiation and phenotypic plasticity in leaf economics spectrum (LES traits, water use efficiency and growth rates under natural and manipulated precipitation regimes in a common garden experiment where seedlings of eight populations of the neotropical live oak Quercus oleoides were established. We also examined the extent to which intraspecific trait variation was associated with plant performance under different water availability. Similar to interspecific patterns among seasonally-dry tropical tree species, live oak populations with long and severe dry seasons had higher leaf nitrogen content and growth rates than mesic populations, which is consistent with a “fast” resource-acquisition strategy aimed to maximize carbon uptake during the wet season. Specific leaf area (SLA was the best predictor of plant performance, but contrary to expectations, it was negatively associated with relative and absolute growth rates. This observation was partially explained by the negative association between SLA and area-based photosynthetic rates, which is contrary to LES expectations but similar to other recent

Beverage-specific mortality relationships in US population data

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Kerr, William C.; Ye, Yu

2011-01-01

Nearly all countries regulate distilled spirits differently from beer and wine. However, the scientific basis for this differential treatment has not been clearly established. This review covers beverage-specific relationships with alcohol-related mortality causes at the population level in the US and includes a new analysis of motor vehicle accident mortality. Spirits were found to be more strongly related to, or the only beverage type with a significant positive association with, cirrhosis, IHD and head and neck cancer mortality. Spirits sales, along with beer, were also implcated in motor vehicle accident mortality and homicde. While all three beverage types were found to be associated with suicide mortality, only spirits had a significant unlagged association. These associations were found under policy arrangements where spirits were discouraged with relatively higher taxes, lower availability and more restricted marketing opportunities. This suggests that the differential policy treatment found in the US and most other countries is justified on the basis of differential harm relationships. PMID:24431476

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

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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.

Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae dengue vector from the Brazilian state of Maranhão

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Andrelina Alves de Sousa

2017-01-01

Full Text Available Aedes (Stegomyia aegypti is the vector responsible for the transmission of the viruses that cause zika, yellow and chikungunya fevers, the four dengue fever serotypes (DENV – 1, 2, 3, 4, and hemorrhagic dengue fever in tropical and subtropical regions around the world. The present study investigated the genetic differentiation of the 15 populations of this vector in the Brazilian state of Maranhão, based on the mitochondrial ND4 marker. A total of 177 sequences were obtained for Aedes aegypti, with a fragment of 337 bps, 15 haplotypes, 15 polymorphics sites, haplotype diversity of h = 0.6938, and nucleotide diversity of π = 0.01486. The neutrality tests (D and Fs were not significant. The AMOVA revealed that most of the variation (58.47% was found within populations, with FST = 0.41533 (p < 0.05. Possible isolation by distance was tested and a significant correlation coefficient (r = 0.3486; p = 0.0040 was found using the Mantel test. The phylogenetic relationships among the 15 haplotypes indicated the existence of two distinct clades. This finding, together with the population parameters, was consistent with a pattern of genetic structuring that underpinned the genetic differentiation of the study populations in Maranhão, and was characterized by the presence of distinct lineages of Aedes aegypti. Keywords: Gene flow, Mitochondrial DNA, ND4

An Alu-like RNA promotes cell differentiation and reduces malignancy of human neuroblastoma cells

OpenAIRE

Castelnuovo Manuele; Massone Sara; Tasso Roberta; Fiorino Gloria; Gatti Monica; Robello Mauro; Gatta Elena; Berger Audrey; Strub Katharina; Florio Tullio; Dieci Giorgio; Cancedda Ranieri; Pagano Aldo

2010-01-01

Neuroblastoma (NB) is a pediatric cancer characterized by remarkable cell heterogeneity within the tumor nodules. Here, we demonstrate that the synthesis of a pol III-transcribed noncoding (nc) RNA (NDM29) strongly restricts NB development by promoting cell differentiation, a drop of malignancy processes, and a dramatic reduction of the tumor initiating cell (TIC) fraction in the NB cell population. Notably, the overexpression of NDM29 also confers to malignant NB cells an unpredicted suscept...

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

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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.

A survey of Sertoli cell differentiation in men after gonadotropin suppression and in testicular cancer

DEFF Research Database (Denmark)

Tarulli, Gerard A; Stanton, Peter G; Loveland, Kate L

2013-01-01

It is widely held that the somatic cell population that is responsible for sperm development and output (Sertoli cells) is terminally differentiated and unmodifiable in adults. It is postulated, with little evidence, that Sertoli cells are not terminally differentiated in some phenotypes of infer...... tubules with CIS and the emergence of strong JAM-A reactivity in seminoma. These findings indicate that adult human Sertoli cells exhibit characteristics of an undifferentiated state in oligospermic men and patients with CIS and seminoma in the presence of germ cell neoplasia....... of infertility and testicular cancer. This study sought to compare markers of Sertoli cell differentiation in normospermic men, oligospermic men (undergoing gonadotropin suppression) and testicular carcinoma in situ (CIS) and seminoma samples. Confocal microscopy was used to assess the expression of markers...... of proliferation (PCNA and Ki67) and functional differentiation (androgen receptor). As additional markers of differentiation, the organization of Sertoli cell tight junction and associated proteins were assessed in specimens with carcinoma in situ. In normal men, Sertoli cells exhibited a differentiated phenotype...

Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range.

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Jean-Baptiste Lamy

Full Text Available BACKGROUND: Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. METHODOLOGY: We assessed cavitation resistance (P(50, growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F(ST and quantitative genetic differentiation (Q(ST, for retrospective identification of the evolutionary forces acting on these traits. RESULTS/DISCUSSION: In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h(2 (ns = 0.43±0.18, CV(A = 4.4%. Q(ST was significantly lower than F(ST, indicating uniform selection for P(50, rather than genetic drift. Putative mechanisms underlying Q(ST

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

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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.

Differential models in ecology

International Nuclear Information System (INIS)

Barco Gomez, Carlos; Barco Gomez, German

2002-01-01

The models mathematical writings with differential equations are used to describe the populational behavior through the time of the animal species. These models can be lineal or no lineal. The differential models for unique specie include the exponential pattern of Malthus and the logistical pattern of Verlhust. The lineal differential models to describe the interaction between two species include the competition relationships, predation and symbiosis

Comparative mortality patterns among the black population and the white-mestizo in Cali and Valle

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Fernando Urrea-Giraldo

2015-08-01

Full Text Available The article analyzes the patterns of comparative mortality of Cali and Valle, between the Afrodescendant and white-mestizo population, by sex and age groups, based on the metadata of deaths in the 2005 Census and the death certificate of the year 2010. The findings reveal strong differentials by age structures of deaths (pyramids and the cumulative mortality, which are conclusive of unequal mortality patterns between the two populations, both in Cali and Valle. This evinces demography of social inequality based on ethnic-racial component.

Pattern of Brain Weight in Three West African Populations

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Clement Vhriterhire

2010-08-01

Full Text Available AIM: The usefulness of brain weight in facilitating proper identification of skeletal remains and in emphasizing a common origin of studied populations is far reaching. METHODS: This study involved 699 (male 361; female 338 volunteers whose age ranged 18 years and over. Respondents were selected along three ethnic groups including Urhobo (male 156; female 147, Ibo (male 141 female 145 and Edo (male 64; female 46 and it was ensured that population for the study was collected using a random stratified method. RESULTS: The brain weight was measured using standard techniques and the mean weight was observed to be 1318g±139.71g with maximum value of 1711.00g and minimum value of 958.42g. Gender had a significant effect on brain weight (p<0.05.Male and female values were significantly different (p<0.05. Mean male values were 1386.18g and mean female values were 1251.62g. Brain weight exhibited strong sexual dimorphism and was useful in differentiating inter and intra population groups. In spite of these observations, differences which enabled intracultural differentiation commonly occurred. CONCLUSION: Inevitably therefore, craniometric studies are most essential in the study of population dynamics especially with respect to quantitative variables. [TAF Prev Med Bull 2010; 9(4.000: 321-324

Migratory patterns and population structure among breeding and wintering red-breasted mergansers (Mergus serrator) and common mergansers (M. merganser)

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Pearce, J.M.; McCracken, K.G.; Christensen, Thomas K.; Zhuravlev, Y.N.

2009-01-01

Philopatry has long been assumed to structure populations of waterfowl and other species of birds genetically, especially via maternally transmitted mitochondrial DNA (mtDNA), yet other migratory behaviors and nesting ecology (use of ground vs. cavity sites) may also contribute to population genetic structure. We investigated the effects of migration and nesting ecology on the population genetic structure of two Holarctic waterfowl, the Red-breasted Merganser (Mergus serrator) and Common Merganser (M. merganser), using mtDNA control-region sequence data. Red-breasted Mergansers (a ground-nesting species) exhibited lower levels of population differentiation across their North American range, possibly as a result of post-Pleistocene range expansion and population growth. By contrast, Common Mergansers (a cavity-nesting species) breeding in western and eastern North America were strongly differentiated, as were continental groups in North America and Europe. Our hypothesis that population differentiation of breeding female Common Mergansers results from limited migration during non-breeding periods was not supported, in that equally heterogeneous mtDNA lineages were observed in males and females on several wintering areas. The interspecific differences in mtDNA patterns for these two closely related species may have resulted from factors related to nesting ecology (ground vs. cavity nesting) and responses to historical climate change.

Strong Migration Limit for Games in Structured Populations: Applications to Dominance Hierarchy and Set Structure

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Dhaker Kroumi

2015-09-01

Full Text Available In this paper, we deduce a condition for a strategy S1 to be more abundant on average at equilibrium under weak selection than another strategy S2 in a population structured into a finite number of colonies of fixed proportions as the population size tends to infinity. It is assumed that one individual reproduces at a time with some probability depending on the payoff received in pairwise interactions within colonies and between colonies and that the offspring replaces one individual chosen at random in the colony into which the offspring migrates. It is shown that an expected weighted average equilibrium frequency of S1 under weak symmetric strategy mutation between S1 and S2 is increased by weak selection if an expected weighted payoff of S1 near neutrality exceeds the corresponding expected weighted payoff of S2. The weights are given in terms of reproductive values of individuals in the different colonies in the neutral model. This condition for S1 to be favoured by weak selection is obtained from a strong migration limit of the genealogical process under neutrality for a sample of individuals, which is proven using a two-time scale argument. The condition is applied to games between individuals in colonies with linear or cyclic dominance and between individuals belonging to groups represented by subsets of a given set.

Differential factors associated with challenge-proven food allergy phenotypes in a population cohort of infants: a latent class analysis.

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Peters, R L; Allen, K J; Dharmage, S C; Lodge, C J; Koplin, J J; Ponsonby, A-L; Wake, M; Lowe, A J; Tang, M L K; Matheson, M C; Gurrin, L C

2015-05-01

Food allergy, eczema and wheeze are early manifestations of allergic disease and commonly co-occur in infancy although their interrelationship is not well understood. Data from population studies are essential to determine whether there are differential drivers of multi-allergy phenotypes. We aimed to define phenotypes and risk factors of allergic disease using latent class analysis (LCA). The HealthNuts study is a prospective, population-based cohort of 5276 12-month-old infants in Melbourne, Australia. LCA was performed using the following baseline data collected at age 12 months: food sensitization (skin prick test ≥ 2 mm) and allergy (oral food challenge) to egg, peanut and sesame; early (food-sensitized eczema (16%), single egg allergy (9%), multiple food allergies (predominantly peanut) (3%) and multiple food allergies (predominantly egg) (2%). Compared to the baseline group of no allergic disease, shared risk factors for all allergic phenotypes were parents born overseas (particularly Asia), delayed introduction of egg, male gender (except for single egg allergy) and family history of allergic disease, whilst exposure to pet dogs was protective for all phenotypes. Other factors including filaggrin mutations, vitamin D and the presence of older siblings differed by phenotype. Multiple outcomes in infancy can be used to determine five distinct allergy phenotypes at the population level, which have both shared and separate risk factors suggesting differential mechanisms of disease. © 2014 John Wiley & Sons Ltd.

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

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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.

Otolith shape: a population marker for Atlantic herring Clupea harengus.

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Libungan, L A; Óskarsson, G J; Slotte, A; Jacobsen, J A; Pálsson, S

2015-04-01

Otolith shape variation of seven Atlantic herring Clupea harengus populations from Canada, the Faroe Islands, Iceland, Ireland, Norway and Scotland, U.K., covering a large area of the species' distribution, was studied in order to see if otolith shape can be used to discriminate between populations. The otolith shape was obtained using quantitative shape analysis, transformed with Wavelet and analysed with multivariate methods. Significant differences were detected among the seven populations, which could be traced to three morphological structures in the otoliths. The differentiation in otolith shape between populations was not only correlated with their spawning time, indicating a strong environmental effect, but could also be due to differing life-history strategies. A model based on the shape differences discriminates with 94% accuracy between Icelandic summer spawners and Norwegian spring spawners, which are known to mix at feeding grounds. This study shows that otolith shape could become an accurate marker for C. harengus population discrimination. © 2015 The Fisheries Society of the British Isles.

The effects of dominance, regular inbreeding and sampling design on Q(ST), an estimator of population differentiation for quantitative traits.

Science.gov (United States)

Goudet, Jérôme; Büchi, Lucie

2006-02-01

To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (F(ST)) and quantitative traits (Q(ST)). If the trait is neutral and its determinism is additive, then theory predicts that Q(ST) = F(ST), while Q(ST) > F(ST) is predicted under directional selection for different local optima, and Q(ST) sampling designs and find that it is always best to sample many populations (>20) with few families (five) rather than few populations with many families. Provided that estimates of Q(ST) are derived from individuals originating from many populations, we conclude that the pattern Q(ST) > F(ST), and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

Mouse V1 population correlates of visual detection rely on heterogeneity within neuronal response patterns

Science.gov (United States)

Montijn, Jorrit S; Goltstein, Pieter M; Pennartz, Cyriel MA

2015-01-01

Previous studies have demonstrated the importance of the primary sensory cortex for the detection, discrimination, and awareness of visual stimuli, but it is unknown how neuronal populations in this area process detected and undetected stimuli differently. Critical differences may reside in the mean strength of responses to visual stimuli, as reflected in bulk signals detectable in functional magnetic resonance imaging, electro-encephalogram, or magnetoencephalography studies, or may be more subtly composed of differentiated activity of individual sensory neurons. Quantifying single-cell Ca2+ responses to visual stimuli recorded with in vivo two-photon imaging, we found that visual detection correlates more strongly with population response heterogeneity rather than overall response strength. Moreover, neuronal populations showed consistencies in activation patterns across temporally spaced trials in association with hit responses, but not during nondetections. Contrary to models relying on temporally stable networks or bulk signaling, these results suggest that detection depends on transient differentiation in neuronal activity within cortical populations. DOI: http://dx.doi.org/10.7554/eLife.10163.001 PMID:26646184

Lack of Population Genetic Structuring in Ocelots (Leopardus pardalis in a Fragmented Landscape

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Marina G. Figueiredo

2015-07-01

Full Text Available Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis, originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars, we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD and Iguaçu Region (IR. Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883. Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i larger effective population size of ocelots (relative to jaguars in each fragment, implying a slower effect of drift-induced differentiation; and (ii potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.

Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management.

Science.gov (United States)

Adin, A; Weber, J C; Sotelo Montes, C; Vidaurre, H; Vosman, B; Smulders, M J M

2004-05-01

Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( Prodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, PPeru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.

Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis as Revealed by Mitochondrial and Microsatellite DNA

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Minmin Chen

2014-06-01

Full Text Available Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS, and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY and Tongling (TL and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP.

Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis) as Revealed by Mitochondrial and Microsatellite DNA

Science.gov (United States)

Chen, Minmin; Zheng, Jinsong; Wu, Min; Ruan, Rui; Zhao, Qingzhong; Wang, Ding

2014-01-01

Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis) is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA) control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS), and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY) and Tongling (TL)) and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP. PMID:24968271

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana).

Science.gov (United States)

Shih, Kai-Ming; Chang, Chung-Te; Chung, Jeng-Der; Chiang, Yu-Chung; Hwang, Shih-Ying

2018-01-01

Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana , disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, F ST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana . Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana , but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana , was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana

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Kai-Ming Shih

2018-02-01

Full Text Available Double digest restriction site-associated DNA sequencing (ddRADseq is a tool for delivering genome-wide single nucleotide polymorphism (SNP markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals of K. davidiana var. formosana. Principal component analysis (PCA, individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE. However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals. This study has produced highly informative population genomic data for the understanding of

Genetic population structure of European sprat (Sprattus sprattus L.): differentiation across a steep environmental gradient in a small pelagic fish

DEFF Research Database (Denmark)

Limborg, Morten; Pedersen, Jes S.; Hansen, Jakob Hemmer

2009-01-01

locations in and around the North- and Baltic Sea area and from a geographically distant population from the Adriatic Sea. Analyses of nine microsatellite loci revealed a sharp genetic division separating samples from the Northeastern Atlantic and the Baltic Sea (pairwise θ = 0.019–0.035), concurring...... with a steep salinity gradient. We found, at most, weak structure among samples within the Northeastern Atlantic region and within the Baltic Sea (pairwise θ = 0.001–0.009). The Adriatic Sea population was highly differentiated from all northern samples (pairwise θ = 0.071–0.092). Overall, the observed...... population structure resembles that of most other marine fishes studied in the North/Baltic Sea areas. Nevertheless, spatially explicit differences are observed among species, likely reflecting specific life-histories. Such fine-scale population structure should be taken into account, e.g. in ecosystem...

Genomic validation of the differential preservation of population history in modern human cranial anatomy.

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Reyes-Centeno, Hugo; Ghirotto, Silvia; Harvati, Katerina

2017-01-01

In modern humans, the significant correlation between neutral genetic loci and cranial anatomy suggests that the cranium preserves a population history signature. However, there is disagreement on whether certain parts of the cranium preserve this signature to a greater degree than other parts. It is also unclear how different quantitative measures of phenotype affect the association of genetic variation and anatomy. Here, we revisit these matters by testing the correlation of genetic distances and various phenotypic distances for ten modern human populations. Geometric morphometric shape data from the crania of adult individuals (n = 224) are used to calculate phenotypic P ST , Procrustes, and Mahalanobis distances. We calculate their correlation to neutral genetic distances, F ST , derived from single nucleotide polymorphisms (SNPs). We subset the cranial data into landmark configurations that include the neurocranium, the face, and the temporal bone in order to evaluate whether these cranial regions are differentially correlated to neutral genetic variation. Our results show that P ST , Mahalanobis, and Procrustes distances are correlated with F ST distances to varying degrees. They indicate that overall cranial shape is significantly correlated with neutral genetic variation. Of the component parts examined, P ST distances for both the temporal bone and the face have a stronger association with F ST distances than the neurocranium. When controlling for population divergence time, only the whole cranium and the temporal bone have a statistically significant association with F ST distances. Our results confirm that the cranium, as a whole, and the temporal bone can be used to reconstruct modern human population history. © 2016 Wiley Periodicals, Inc.

Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States.

Science.gov (United States)

Tabima, Javier F; Coffey, Michael D; Zazada, Inga A; Grünwald, Niklaus J

2018-04-11

Population genetics is a powerful tool to understand patterns and evolutionary processes that are involved in plant-pathogen emergence and adaptation to agricultural ecosystems. We are interested in studying the population dynamics of Phytophthora rubi, the causal agent of Phytophthora root rot in raspberry. P. rubi is found in the western United States, where most of the fresh and processed raspberries are produced. We used genotyping-by-sequencing to characterize genetic diversity in populations of P. rubi sampled in the United States and other countries. Our results confirm that P. rubi is a monophyletic species with complete lineage sorting from its sister taxon P. fragariae. Overall, populations of P. rubi show low genetic diversity across the western United States. Demographic analyses suggest that populations of P. rubi from the western United States are the source of pathogen migration to Europe. We found no evidence for population differentiation at a global or regional (western United States) level. Finally, our results provide evidence of migration from California and Oregon into Washington. This report provides new insights into the evolution and structure of global and western United States populations of the raspberry pathogen P. rubi, indicating that human activity might be involved in moving the pathogen among regions and fields.

Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country.

Science.gov (United States)

Pumpaibool, Tepanata; Arnathau, Céline; Durand, Patrick; Kanchanakhan, Naowarat; Siripoon, Napaporn; Suegorn, Aree; Sitthi-Amorn, Chitr; Renaud, François; Harnyuttanakorn, Pongchai

2009-07-14

The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites). Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 +/- 0.17), where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai populations during this study. Comparison of the genetic

The Effect of Recurrent Floods on Genetic Composition of Marble Trout Populations

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Pujolar, José Martin; Vincenzi, Simone; Zane, Lorenzo; Jesensek, Dusan; De Leo, Giulio A.; Crivelli, Alain J.

2011-01-01

A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global F ST of 0.716), which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3–4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change. PMID:21931617

Phylogeography and Genetic Differentiation among Populations of the Moon Turban Snail Lunella granulata Gmelin, 1791 (Gastropoda: Turbinidae

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Chuen-Tan Jean

2013-04-01

Full Text Available We examined the genetic variation and phylogeographic relationships among 10 populations of Lunella granulata from mainland China, Penghu Archipelago, Taiwan Island, and Japan using mitochondrial COI and 16S markers. A total of 45 haplotypes were obtained in 112 specimens, and relatively high levels of haplotype diversity (h = 0.903 and low levels of nucleotide diversity (π = 0.0046 were detected. Four major phylogenetic lineage clusters were revealed and were concordant with their geographic distribution, agreeing with the haplotype network. These results suggested that geographic barrier isolating effects were occurring among the populations. This hypothesis was also supported by a significant genetic differentiation index (FST = 0.709 and by a spatial analysis of molecular variance (SAMOVA analysis. A mismatch distribution analysis, neutrality tests and Bayesian skyline plots found a single significant population expansion. This expansion occurred on the coast of mainland China before 20–17 ka. Consequently, although the dispersal ability of the planktonic stage and the circulation of ocean currents generally promote genetic exchanges among populations, L. granulata has tended to maintain distinct genetic groups that reflect the respective geographic origins of the constituent lineages. Although the circulation of ocean currents, in principle, may still play a role in determining the genetic composition of populations, long-distance migration between regions is difficult even at the planktonic stage.

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

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de Oliveira, Thais C; Rodrigues, Priscila T; Menezes, Maria José; Gonçalves-Lopes, Raquel M; Bastos, Melissa S; Lima, Nathália F; Barbosa, Susana; Gerber, Alexandra L; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R; Alves, João Marcelo P; Ferreira, Marcelo U

2017-07-01

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 diverse sites

The endoperoxide ascaridol shows strong differential cytotoxicity in nucleotide excision repair-deficient cells

Energy Technology Data Exchange (ETDEWEB)

Abbasi, Rashda [Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Efferth, Thomas [Institute of Pharmacy und Biochemistry, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz (Germany); Kuhmann, Christine [Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Opatz, Till [Institute of Organic Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz (Germany); Hao, Xiaojiang [Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204 (China); Popanda, Odilia, E-mail: o.popanda@dkfz.de [Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany); Schmezer, Peter [Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)

2012-03-15

Targeting synthetic lethality in DNA repair pathways has become a promising anti-cancer strategy. However little is known about such interactions with regard to the nucleotide excision repair (NER) pathway. Therefore, cell lines with a defect in the NER genes ERCC6 or XPC and their normal counterparts were screened with 53 chemically defined phytochemicals isolated from plants used in traditional Chinese medicine for differential cytotoxic effects. The screening revealed 12 drugs that killed NER-deficient cells more efficiently than proficient cells. Five drugs were further analyzed for IC{sub 50} values, effects on cell cycle distribution, and induction of DNA damage. Ascaridol was the most effective compound with a difference of > 1000-fold in resistance between normal and NER-deficient cells (IC{sub 50} values for cells with deficiency in ERCC6: 0.15 μM, XPC: 0.18 μM, and normal cells: > 180 μM). NER-deficiency combined with ascaridol treatment led to G2/M-phase arrest, an increased percentage of subG1 cells, and a substantially higher DNA damage induction. These results were confirmed in a second set of NER-deficient and -proficient cell lines with isogenic background. Finally, ascaridol was characterized for its ability to generate oxidative DNA damage. The drug led to a dose-dependent increase in intracellular levels of reactive oxygen species at cytotoxic concentrations, but only NER-deficient cells showed a strongly induced amount of 8-oxodG sites. In summary, ascaridol is a cytotoxic and DNA-damaging compound which generates intracellular reactive oxidative intermediates and which selectively affects NER-deficient cells. This could provide a new therapeutic option to treat cancer cells with mutations in NER genes. -- Highlights: ► Thousand-fold higher Ascaridol activity in NER-deficient versus proficient cells. ► Impaired repair of Ascaridol-induced oxidative DNA damage in NER-deficient cells. ► Selective activity of Ascaridol opens new therapy

The endoperoxide ascaridol shows strong differential cytotoxicity in nucleotide excision repair-deficient cells

International Nuclear Information System (INIS)

Abbasi, Rashda; Efferth, Thomas; Kuhmann, Christine; Opatz, Till; Hao, Xiaojiang; Popanda, Odilia; Schmezer, Peter

2012-01-01

Targeting synthetic lethality in DNA repair pathways has become a promising anti-cancer strategy. However little is known about such interactions with regard to the nucleotide excision repair (NER) pathway. Therefore, cell lines with a defect in the NER genes ERCC6 or XPC and their normal counterparts were screened with 53 chemically defined phytochemicals isolated from plants used in traditional Chinese medicine for differential cytotoxic effects. The screening revealed 12 drugs that killed NER-deficient cells more efficiently than proficient cells. Five drugs were further analyzed for IC 50 values, effects on cell cycle distribution, and induction of DNA damage. Ascaridol was the most effective compound with a difference of > 1000-fold in resistance between normal and NER-deficient cells (IC 50 values for cells with deficiency in ERCC6: 0.15 μM, XPC: 0.18 μM, and normal cells: > 180 μM). NER-deficiency combined with ascaridol treatment led to G2/M-phase arrest, an increased percentage of subG1 cells, and a substantially higher DNA damage induction. These results were confirmed in a second set of NER-deficient and -proficient cell lines with isogenic background. Finally, ascaridol was characterized for its ability to generate oxidative DNA damage. The drug led to a dose-dependent increase in intracellular levels of reactive oxygen species at cytotoxic concentrations, but only NER-deficient cells showed a strongly induced amount of 8-oxodG sites. In summary, ascaridol is a cytotoxic and DNA-damaging compound which generates intracellular reactive oxidative intermediates and which selectively affects NER-deficient cells. This could provide a new therapeutic option to treat cancer cells with mutations in NER genes. -- Highlights: ► Thousand-fold higher Ascaridol activity in NER-deficient versus proficient cells. ► Impaired repair of Ascaridol-induced oxidative DNA damage in NER-deficient cells. ► Selective activity of Ascaridol opens new therapy options in

CT differentiation of poorly-differentiated gastric neuroendocrine tumours from well-differentiated neuroendocrine tumours and gastric adenocarcinomas

Energy Technology Data Exchange (ETDEWEB)

Kim, Seong Ho; Kim, Se Hyung; Shin, Cheong-il; Han, Joon Koo; Choi, Byung Ihn [Seoul National University Hospital, Department of Radiology, Jongno-gu, Seoul (Korea, Republic of); Seoul National University Hospital, Institute of Radiation Medicine, Jongno-gu, Seoul (Korea, Republic of); Kim, Min-A [Seoul National University Hospital, Department of Pathology, Jongno-gu, Seoul (Korea, Republic of)

2015-07-15

To evaluate the differential CT features of gastric poorly-differentiated neuroendocrine tumours (PD-NETs) from well-differentiated NETs (WD-NETs) and gastric adenocarcinomas (ADCs) and to suggest differential features of hepatic metastases from gastric NETs and ADCs. Our study population was comprised of 36 patients with gastric NETs (18 WD-NETs, 18 PD-NETs) and 38 patients with gastric ADCs who served as our control group. Multiple CT features were assessed to identify significant differential CT findings of PD-NETs from WD-NETs and ADCs. In addition, CT features of hepatic metastases including the metastasis-to-liver ratio were analyzed to differentiate metastatic NETs from ADCs. The presence of metastatic lymph nodes was the sole differentiator of PD-NETs from WD-NETs (P =.001, odds ratio = 56.67), while the presence of intact overlying mucosa with mucosal tenting was the sole significant CT feature differentiating PD-NETs from ADCs (P =.047, odds ratio = 15.3) For hepatic metastases, metastases from NETs were more hyper-attenuated than those from ADCs. The presence of metastatic LNs and intact overlying mucosa with mucosal tenting are useful CT discriminators of PD-NETs from WD-NETs and ADCs, respectively. In addition, a higher metastasis-to-liver ratio may help differentiate hepatic metastases of gastric NETs from those of gastric ADCs with high accuracy. (orig.)

Growth anomalies on the coral genera Acropora and Porites are strongly associated with host density and human population size across the Indo-Pacific.

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Greta S Aeby

2011-02-01

Full Text Available Growth anomalies (GAs are common, tumor-like diseases that can cause significant morbidity and decreased fecundity in the major Indo-Pacific reef-building coral genera, Acropora and Porites. GAs are unusually tractable for testing hypotheses about drivers of coral disease because of their pan-Pacific distributions, relatively high occurrence, and unambiguous ease of identification. We modeled multiple disease-environment associations that may underlie the prevalence of Acropora growth anomalies (AGA (n = 304 surveys and Porites growth anomalies (PGA (n = 602 surveys from across the Indo-Pacific. Nine predictor variables were modeled, including coral host abundance, human population size, and sea surface temperature and ultra-violet radiation anomalies. Prevalence of both AGAs and PGAs were strongly host density-dependent. PGAs additionally showed strong positive associations with human population size. Although this association has been widely posited, this is one of the first broad-scale studies unambiguously linking a coral disease with human population size. These results emphasize that individual coral diseases can show relatively distinct patterns of association with environmental predictors, even in similar diseases (growth anomalies found on different host genera (Acropora vs. Porites. As human densities and environmental degradation increase globally, the prevalence of coral diseases like PGAs could increase accordingly, halted only perhaps by declines in host density below thresholds required for disease establishment.

Growth anomalies on the coral genera Acropora and Porites are strongly associated with host density and human population size across the Indo-Pacific

Science.gov (United States)

Aeby, Greta S.; Williams, Gareth J.; Franklin, Erik C.; Haapkyla, Jessica; Harvell, C. Drew; Neale, Stephen; Page, Cathie A.; Raymundo, Laurie; Vargas-Angel, Bernardo; Willis, Bette L.; Work, Thierry M.; Davy, Simon K.

2011-01-01

Growth anomalies (GAs) are common, tumor-like diseases that can cause significant morbidity and decreased fecundity in the major Indo-Pacific reef-building coral genera, Acropora and Porites. GAs are unusually tractable for testing hypotheses about drivers of coral disease because of their pan-Pacific distributions, relatively high occurrence, and unambiguous ease of identification. We modeled multiple disease-environment associations that may underlie the prevalence of Acropora growth anomalies (AGA) (n = 304 surveys) and Porites growth anomalies (PGA) (n = 602 surveys) from across the Indo-Pacific. Nine predictor variables were modeled, including coral host abundance, human population size, and sea surface temperature and ultra-violet radiation anomalies. Prevalence of both AGAs and PGAs were strongly host density-dependent. PGAs additionally showed strong positive associations with human population size. Although this association has been widely posited, this is one of the first broad-scale studies unambiguously linking a coral disease with human population size. These results emphasize that individual coral diseases can show relatively distinct patterns of association with environmental predictors, even in similar diseases (growth anomalies) found on different host genera (Acropora vs. Porites). As human densities and environmental degradation increase globally, the prevalence of coral diseases like PGAs could increase accordingly, halted only perhaps by declines in host density below thresholds required for disease establishment.

Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen.

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Simren Brar

Full Text Available White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales. This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.

Diagnosing avian influenza infection in vaccinated populations by systems for differentiating infected from vaccinated animals (DIVA).

Science.gov (United States)

Capua, I; Cattoli, G

2007-01-01

Vaccination against avian influenza is recommended as a tool to support control measures in countries affected by avian influenza. Vaccination is known to increase the resistance of susceptible birds to infection and also to reduce shedding; however, it does not always prevent infection. Vaccinated infected flocks can therefore be a source of infection and thus be responsible for the perpetuation of infection. To avoid the spread of infection in a vaccinated population, immunization strategies must allow differentiation of infected from vaccinated animals (DIVA), combined with an appropriate monitoring system. Vaccinated exposed flocks must be identified and managed by restriction policies that include controlled marketing and stamping-out. Several vaccines and diagnostic tests to detect infection in vaccinated populations are available, the tests having various properties and characteristics. In order to achieve eradication, the most appropriate DIVA vaccination strategy must be identified and an appropriate monitoring programme be designed, taking into account risk factors, the epidemiological situation and the socioeconomic implications of the policy.

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

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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

Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis.

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Bing-Jian Liu

Full Text Available The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2. Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource.

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

International Nuclear Information System (INIS)

Özmen, Evrim; Adaletli, İbrahim; Kayadibi, Yasemin; Emre, Şenol; Kılıç, Fahrettin; Dervişoğlu, Sergülen; Kuruğoğlu, Sebuh; Şenyüz, Osman Faruk

2014-01-01

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

Genomic evidence for the population genetic differentiation of Misgurnus anguillicaudatus in the Yangtze River basin of China.

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Yi, Shaokui; Wang, Weimin; Zhou, Xiaoyun

2018-02-21

Misgurnus anguillicaudatus, an important aquatic species, is mainly distributed in the Yangtze River basin. To reveal the population genetic structure of M. anguillicaudatus distributed in the Yangtze River basin, genotyping by sequencing (GBS) technique was employed to detect the genome wide genetic variations of M. anguillicaudatus. A total of 30.03 Gb raw data were yielded from 70 samples collected from 15 geographic sites located in the Yangtze River basin. Subsequently, 2092 high quality SNPs were genotyped across these samples and used for a series of genetic analysis. The results of genetic analysis showed that high levels of genetic diversity were observed and the populations from upper reaches (UR) were significantly differentiated from the middle and lower reaches (MLR) of Yangtze River basin. Meanwhile, no significant isolation by distance was detected among the populations. Ecological factors (e.g. complicated topography and climatic environment) and anthropogenic factors (e.g. aquaculture and agriculture cultivation) might account for the genetic disconnectivity between UR and MLR populations. This study provided valuable genetic data for the future breeding program and also for the conversation and scientific utilization of those abundant genetic resources stored in the Yangtze River basin. Copyright © 2018 Elsevier Inc. All rights reserved.

Moving Upstream in U.S. Hospital Care Toward Investments in Population Health.

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Begun, James W; Potthoff, Sandra

The root causes for most health outcomes are often collectively referred to as the social determinants of health. Hospitals and health systems now must decide how much to "move upstream," or invest in programs that directly affect the social determinants of health. Moving upstream in healthcare delivery requires an acceptance of responsibility for the health of populations. We examine responses of 950 nonfederal, general hospitals in the United States to the 2015 American Hospital Association Population Health Survey to identify characteristics that distinguish those hospitals that are most aligned with population health and most engaged in addressing social determinants of health. Those "upstream" hospitals are significantly more likely to be large, not-for-profit, metropolitan, teaching-affiliated, and members of systems. Internally, the more upstream hospitals are more likely to organize their population health activities with strong executive-level involvement, full-time-equivalent support, and coordination at the system level.The characteristics differentiating hospitals strongly involved in population health and upstream activity are not unlike those characteristics associated with diffusion of many innovations in hospitals. These hospitals may be the early adopters in a diffusion process that will eventually include most hospitals or, at least, most not-for-profit hospitals. Alternatively, the population health and social determinants movements could be transient or could be limited to a small portion of hospitals such as those identified here, with distinctive patient populations, missions, and resources.

The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler.

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Wright, David J; Spurgin, Lewis G; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

2014-05-01

Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Symmetries of stochastic differential equations: A geometric approach

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De Vecchi, Francesco C., E-mail: francesco.devecchi@unimi.it; Ugolini, Stefania, E-mail: stefania.ugolini@unimi.it [Dipartimento di Matematica, Università degli Studi di Milano, via Saldini 50, Milano (Italy); Morando, Paola, E-mail: paola.morando@unimi.it [DISAA, Università degli Studi di Milano, via Celoria 2, Milano (Italy)

2016-06-15

A new notion of stochastic transformation is proposed and applied to the study of both weak and strong symmetries of stochastic differential equations (SDEs). The correspondence between an algebra of weak symmetries for a given SDE and an algebra of strong symmetries for a modified SDE is proved under suitable regularity assumptions. This general approach is applied to a stochastic version of a two dimensional symmetric ordinary differential equation and to the case of two dimensional Brownian motion.

A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus).

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Ferchaud, Anne-Laure; Pedersen, Susanne H; Bekkevold, Dorte; Jian, Jianbo; Niu, Yongchao; Hansen, Michael M

2014-10-06

The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background. RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new. We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

Great genetic differentiation among populations of Meconopsis integrifolia and its implication for plant speciation in the Qinghai-Tibetan Plateau.

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Fu-Sheng Yang

Full Text Available The complex tectonic events and climatic oscillations in the Qinghai-Tibetan Plateau (QTP, the largest and highest plateau in the world, are thought to have had great effects on the evolutionary history of the native plants. Of great interest is to investigate plant population genetic divergence in the QTP and its correlation with the geologic and climatic changes. We conducted a range-wide phylogeographical analysis of M. integrifolia based on the chloroplast DNA (cpDNA trnL-trnF and trnfM-trnS regions, and defined 26 haplotypes that were phylogenetically divided into six clades dated to the late Tertiary. The six clades correspond, respectively, to highly differentiated population groups that do not overlap in geographic distribution, implying that the mountain ranges acting as corridors or barriers greatly affected the evolutionary history of the QTP plants. The older clade of M. integrifolia only occurs in the southwest of the species' range, whereas the distributions of younger clades extend northeastward in the eastern QTP, suggesting that climatic divergence resulting from the uplift of the QTP triggered the initial divergence of M. integrifolia native to the plateau. Also, the nrDNA ITS region was used to clarify the unexpected phylogenetic relationships of cpDNA haplotypes between M. integrifolia and M. betonicifolia. The topological incongruence between the two phylogenies suggests an ancestral hybridization between the two species. Our study indicates that geographic isolation and hybridization are two important mechanisms responsible for the population differentiation and speciation of Meconopsis, a species-rich genus with complex polyploids.

Bioactive glass ions as strong enhancers of osteogenic differentiation in human adipose stem cells.

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Ojansivu, Miina; Vanhatupa, Sari; Björkvik, Leena; Häkkänen, Heikki; Kellomäki, Minna; Autio, Reija; Ihalainen, Janne A; Hupa, Leena; Miettinen, Susanna

2015-07-01

Bioactive glasses are known for their ability to induce osteogenic differentiation of stem cells. To elucidate the mechanism of the osteoinductivity in more detail, we studied whether ionic extracts prepared from a commercial glass S53P4 and from three experimental glasses (2-06, 1-06 and 3-06) are alone sufficient to induce osteogenic differentiation of human adipose stem cells. Cells were cultured using basic medium or osteogenic medium as extract basis. Our results indicate that cells stay viable in all the glass extracts for the whole culturing period, 14 days. At 14 days the mineralization in osteogenic medium extracts was excessive compared to the control. Parallel to the increased mineralization we observed a decrease in the cell amount. Raman and Laser Induced Breakdown Spectroscopy analyses confirmed that the mineral consisted of calcium phosphates. Consistently, the osteogenic medium extracts also increased osteocalcin production and collagen Type-I accumulation in the extracellular matrix at 13 days. Of the four osteogenic medium extracts, 2-06 and 3-06 induced the best responses of osteogenesis. However, regardless of the enhanced mineral formation, alkaline phosphatase activity was not promoted by the extracts. The osteogenic medium extracts could potentially provide a fast and effective way to differentiate human adipose stem cells in vitro. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Induction of osteogenic markers in differentially treated cultures of embryonic stem cells

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Ommerborn Michelle A

2008-06-01

Full Text Available Abstract Background Facial trauma or tumor surgery in the head and face area often lead to massive destruction of the facial skeleton. Cell-based bone reconstruction therapies promise to offer new therapeutic opportunities for the repair of bone damaged by disease or injury. Currently, embryonic stem cells (ESCs are discussed to be a potential cell source for bone tissue engineering. The purpose of this study was to investigate various supplements in culture media with respect to the induction of osteogenic differentiation. Methods Murine ESCs were cultured in the presence of LIF (leukemia inhibitory factor, DAG (dexamethasone, ascorbic acid and β-glycerophosphate or bone morphogenetic protein-2 (BMP-2. Microscopical analyses were performed using von Kossa staining, and expression of osteogenic marker genes was determined by real time PCR. Results ESCs cultured with DAG showed by far the largest deposition of calcium phosphate-containing minerals. Starting at day 9 of culture, a strong increase in collagen I mRNA expression was detected in the DAG-treated cells. In BMP-2-treated ESCs the collagen I mRNA induction was less increased. Expression of osteocalcin, a highly specific marker for osteogentic differentiation, showed a double-peaked curve in DAG-treated cells. ESCs cultured in the presence of DAG showed a strong increase in osteocalcin mRNA at day 9 followed by a second peak starting at day 17. Conclusion Supplementation of ESC cell cultures with DAG is effective in inducing osteogenic differentiation and appears to be more potent than stimulation with BMP-2 alone. Thus, DAG treatment can be recommended for generating ESC populations with osteogenic differentiation that are intended for use in bone tissue engineering.

Pseudo-differentiation syndrome

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Fathi Jehani

2011-01-01

Full Text Available

A patient with relapsed acute myeloid leukemia (<strong>AMLstrong> (M2 FAB classification developed a differentiating syndrome upon receiving Decitabine therapy given with palliative intent. The patient presented with high grade fever, constitutional symptoms and severe chest symptoms with no underlying lung condition. Chest x-ray (CXR showed diffuse pulmonary infiltrates. Septic work up followed by intravenous broad spectrum antimicrobials did not improve his condition. Pan cultures’ results were repeatedly negative. Treatment with high dose Dexamethasone (DXM resulted in marked clinical and radiological improvement.

Our patient initially presented with relapsed AML (M2 Fab classification with t (8; 21; negative FMS-like tyrosine kinase -internal tandem duplication (FLT3-ITD which are all good prognostic factors, yet the patient had an atypical clinical course with early frequent relapses, differentiation syndrome associated with Decitabine therapy and late in his disease, he developed a granulocytic sarcoma.<strong style="mso-bidi-font-weight: normal;">strong>

Simultaneous determination of seven informative Y chromosome SNPs to differentiate East Asian, European, and African populations.

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Muro, Tomonori; Iida, Reiko; Fujihara, Junko; Yasuda, Toshihiro; Watanabe, Yukina; Imamura, Shinji; Nakamura, Hiroaki; Kimura-Kataoka, Kaori; Yuasa, Isao; Toga, Tomoko; Takeshita, Haruo

2011-05-01

Identification of the population origin of an individual is very useful for crime investigators who need to narrow down a suspect based on specimens left at a crime scene. Single nucleotide polymorphisms of the Y chromosome (Y-SNPs) are a class of markers of interest to forensic investigators because many of the markers indicate regional specificity, thus providing useful information about the geographic origin of a subject. We selected seven informative Y-SNPs (M168, M130, JST021355, M96, P126, P196, and P234) to differentiate the three major population groups (East Asian, European, and African) and used them to develop forensic application. SNP genotyping was carried out by multiplex PCR reaction and multiplex single base extension (MSBE) reaction followed by capillary electrophoresis of extension products. This method can be used to assign a haplogroup from both degraded male DNA samples and DNA samples containing a mixture of female and male DNA through PCR primers that generate small amplicons (less than about 150 bp) and are highly specific for targets on the Y chromosome. The allelic state of each marker was definitively determined from a total of 791 males from the three major population groups. As expected, samples from the three major population groups showed Y-haplogroups common in the region of provenance: Y haplogroups C, D, and O for East Asians; IJ and R1 for Europeans; and AB and E for Africans. Published by Elsevier Ireland Ltd.

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

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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.

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

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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.

Comparative morphometrics of two populations of Mugil curema (Pisces: Mugilidae on the Atlantic and Mexican Pacific coasts

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Ana Laura Ibáñez-Aguirre

2006-03-01

Full Text Available A population of Mugil curema in the Gulf of Mexico was compared with one in the Pacific Ocean using nine morphometric variables. The allometries of each measurement were estimated in relation to total length. Morphometric variations were analyzed using the normalization of the individuals of each group and two multivariate methods: correspondence analysis, used to explore the information, and discriminant analysis. Results indicated that the diameter of the eye differentiated the populations of both coasts, the Atlantic population showed a larger eye diameter. However, other than this and the body width (which can be strongly influenced by sexual maturation there was no difference between the shapes of both populations. We discuss the larger morphometric variability of the Atlantic population which may be due to the presence of more than one population unlike the Pacific population.

CENTRAL DARK MATTER TRENDS IN EARLY-TYPE GALAXIES FROM STRONG LENSING, DYNAMICS, AND STELLAR POPULATIONS

International Nuclear Information System (INIS)

Tortora, C.; Jetzer, P.; Napolitano, N. R.; Romanowsky, A. J.

2010-01-01

We analyze the correlations between central dark matter (DM) content of early-type galaxies and their sizes and ages, using a sample of intermediate-redshift (z ∼ 0.2) gravitational lenses from the SLACS survey, and by comparing them to a larger sample of z ∼ 0 galaxies. We decompose the deprojected galaxy masses into DM and stellar components using combinations of strong lensing, stellar dynamics, and stellar populations modeling. For a given stellar mass, we find that for galaxies with larger sizes, the DM fraction increases and the mean DM density decreases, consistently with the cuspy halos expected in cosmological formation scenarios. The DM fraction also decreases with stellar age, which can be partially explained by the inverse correlation between size and age. The residual trend may point to systematic dependencies on formation epoch of halo contraction or stellar initial mass functions. These results are in agreement with recent findings based on local galaxies by Napolitano et al. and suggest negligible evidence of galaxy evolution over the last ∼2.5 Gyr other than passive stellar aging.

Floral contrivances and specialised pollination mechanism strongly influence mixed mating in Wrightia tomentosa (Apocynaceae).

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Barman, C; Singh, V K; Das, S; Tandon, R

2018-05-01

Reproductive success of a plant species is largely influenced by the outcome of mating pattern in a population. It is believed that a significantly larger proportion of animal-pollinated plants have evolved a mixed-mating strategy, the extent of which may vary among species. It is thus pertinent to investigate the key contributors to mating success, especially to identify the reproductive constraints in depauperate populations of threatened plant species. We examined the contribution of floral architecture, pollination mechanism and breeding system on the extent of outcrossing rate in a near-threatened tree species, Wrightia tomentosa. The breeding system was ascertained from controlled pollination experiments. In order to determine outcrossing rate, 60 open-pollinated progeny were analysed using an AFLP markers. Although the trees are self-compatible, herkogamy and compartmentalisation of pollen and nectar in different chambers of the floral tube effectively prevent spontaneous autogamy. Pollination is achieved through specialised interaction with moths. Differential foraging behaviour of settling moths and hawkmoths leads to different proportions of geitonogamous and xenogamous pollen on the stigma. However, most open-pollinated progeny were the result of xenogamy (outcrossing rate, tm = 0.68). The study shows that floral contrivances and pollination system have a strong influence on mating pattern. The differential foraging behaviour of the pollinators causes deposition of a mixture of self- and cross-pollen to produce a mixed brood. Inbreeding depression and geitonogamy appear to play a significant role in sustaining mixed mating in this species. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Second order approximation for optical polaron in the strong coupling case

International Nuclear Information System (INIS)

Bogolubov, N.N. Jr.

1993-11-01

Here we propose a method of construction second order approximation for ground state energy for class of model Hamiltonian with linear type interaction on Bose operators in strong coupling case. For the application of the above method we have considered polaron model and propose construction set of nonlinear differential equations for definition ground state energy in strong coupling case. We have considered also radial symmetry case. (author). 10 refs

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

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. 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. Concentrations of total leukocytes, neutrophils and lymphocytes are associated with incidence of diabetes. However, the lack of association with the R262W polymorphism suggests that the associations

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

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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.

Virtual detector theory for strong-field atomic ionization

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Wang, Xu; Tian, Justin; Eberly, J. H.

2018-04-01

A virtual detector (VD) is an imaginary device located at a fixed position in space that extracts information from the wave packet passing through it. By recording the particle momentum and the corresponding probability current at each time, the VDs can accumulate and build the differential momentum distribution of the particle, in a way that resembles real experiments. A mathematical proof is given for the equivalence of the differential momentum distribution obtained by the VD method and by Fourier transforming the wave function. In addition to being a tool for reducing the computational load, VDs have also been found useful in interpreting the ultrafast strong-field ionization process, especially the controversial quantum tunneling process.

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

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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

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

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de Oliveira, Thais C.; Rodrigues, Priscila T.; Menezes, Maria José; Gonçalves-Lopes, Raquel M.; Bastos, Melissa S.; Lima, Nathália F.; Barbosa, Susana; Gerber, Alexandra L.; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R.

2017-01-01

Background 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. Methods 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). Principal findings/Conclusions 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

Highly Resolved Measurements of a Developing Strong Collisional Plasma Shock

Science.gov (United States)

Rinderknecht, Hans G.; Park, H.-S.; Ross, J. S.; Amendt, P. A.; Higginson, D. P.; Wilks, S. C.; Haberberger, D.; Katz, J.; Froula, D. H.; Hoffman, N. M.; Kagan, G.; Keenan, B. D.; Vold, E. L.

2018-03-01

The structure of a strong collisional shock front forming in a plasma is directly probed for the first time in laser-driven gas-jet experiments. Thomson scattering of a 526.5 nm probe beam was used to diagnose temperature and ion velocity distribution in a strong shock (M ˜11 ) propagating through a low-density (ρ ˜0.01 mg /cc ) plasma composed of hydrogen. A forward-streaming population of ions traveling in excess of the shock velocity was observed to heat and slow down on an unmoving, unshocked population of cold protons, until ultimately the populations merge and begin to thermalize. Instabilities are observed during the merging, indicating a uniquely plasma-phase process in shock front formation.

Differential response of two sourgrass populations to glyphosate

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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.

Differential gene expression during Trypanosoma cruzi metacyclogenesis

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Marco Aurelio Krieger

1999-09-01

Full Text Available The transformation of epimastigotes into metacyclic trypomastigotes involves changes in the pattern of expressed genes, resulting in important morphological and functional differences between these developmental forms of Trypanosoma cruzi. In order to identify and characterize genes involved in triggering the metacyclogenesis process and in conferring to metacyclic trypomastigotes their stage specific biological properties, we have developed a method allowing the isolation of genes specifically expressed when comparing two close related cell populations (representation of differential expression or RDE. The method is based on the PCR amplification of gene sequences selected by hybridizing and subtracting the populations in such a way that after some cycles of hybridization-amplification genes specific to a given population are highly enriched. The use of this method in the analysis of differential gene expression during T. cruzi metacyclogenesis (6 hr and 24 hr of differentiation and metacyclic trypomastigotes resulted in the isolation of several clones from each time point. Northern blot analysis showed that some genes are transiently expressed (6 hr and 24 hr differentiating cells, while others are present in differentiating cells and in metacyclic trypomastigotes. Nucleotide sequencing of six clones characterized so far showed that they do not display any homology to gene sequences available in the GeneBank.

Immune gene expression in Bombus terrestris: signatures of infection despite strong variation among populations, colonies, and sister workers.

Directory of Open Access Journals (Sweden)

Franziska S Brunner

Full Text Available Ecological immunology relies on variation in resistance to parasites. Colonies of the bumblebee Bombus terrestris vary in their susceptibility to the trypanosome gut parasite Crithidia bombi, which reduces colony fitness. To understand the possible origin of this variation in resistance we assayed the expression of 28 immunologically important genes in foraging workers. We deliberately included natural variation of the host "environment" by using bees from colonies collected in two locations and sampling active foraging workers that were not age controlled. Immune gene expression patterns in response to C. bombi showed remarkable variability even among genetically similar sisters. Nevertheless, expression varied with parasite exposure, among colonies and, perhaps surprisingly, strongly among populations (collection sites. While only the antimicrobial peptide abaecin is universally up regulated upon exposure, linear discriminant analysis suggests that the overall exposure effect is driven by a combination of several immune pathways and further immune functions such as ROS regulation. Also, the differences among colonies in their immune gene expression profiles provide clues to the mechanistic basis of well-known inter-colony variation in susceptibility to this parasite. Our results show that transcriptional responses to parasite exposure can be detected in ecologically heterogeneous groups despite strong background noise.

Strong profiling is not mathematically optimal for discovering rare malfeasors

Energy Technology Data Exchange (ETDEWEB)

Press, William H [Los Alamos National Laboratory

2008-01-01

In a large population of individuals labeled j = 1,2,...,N, governments attempt to find the rare malfeasor j = j, (terrorist, for example) by making use of priors p{sub j} that estimate the probability of individual j being a malfeasor. Societal resources for secondary random screening such as airport search or police investigation are concentrated against individuals with the largest priors. They may call this 'strong profiling' if the concentration is at least proportional to p{sub j} for the largest values. Strong profiling often results in higher probability, but otherwise innocent, individuals being repeatedly subjected to screening. They show here that, entirely apart from considerations of social policy, strong profiling is not mathematically optimal at finding malfeasors. Even if prior probabilities were accurate, their optimal use would be only as roughly the geometric mean between a strong profiling and a completely uniform sampling of the population.

Rapid divergence of mussel populations despite incomplete barriers to dispersal.

Science.gov (United States)

Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia L; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul Hamid A; Gillespie, Rosemary G; Becking, Leontine E

2018-04-01

Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence. © 2018 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Characterization of strong (241)Am sources.

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Vesterlund, Anna; Chernikova, Dina; Cartemo, Petty; Axell, Kåre; Nordlund, Anders; Skarnemark, Gunnar; Ekberg, Christian; Ramebäck, Henrik

2015-05-01

Gamma ray spectra of strong (241)Am sources may reveal information about the source composition as there may be other radioactive nuclides such as progeny and radioactive impurities present. In this work the possibility to use gamma spectrometry to identify inherent signatures in (241)Am sources in order to differentiate sources from each other, is investigated. The studied signatures are age, i.e. time passed since last chemical separation, and presence of impurities. The spectra of some sources show a number of Doppler broadened peaks in the spectrum which indicate the presence of nuclear reactions on light elements within the sources. The results show that the investigated sources can be differentiated between by age and/or presence of impurities. These spectral features would be useful information in a national nuclear forensics library (NNFL) in cases when the visual information on the source, e.g. the source number, is unavailable. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

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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

GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

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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.

Neighborhood deprivation is strongly associated with participation in a population-based health check

DEFF Research Database (Denmark)

Bender, Anne Mette; Kawachi, Ichiro; Jørgensen, Torben

2015-01-01

BACKGROUND: We sought to examine whether neighborhood deprivation is associated with participation in a large population-based health check. Such analyses will help answer the question whether health checks, which are designed to meet the needs of residents in deprived neighborhoods, may increase...... participation and prove to be more effective in preventing disease. In Europe, no study has previously looked at the association between neighborhood deprivation and participation in a population-based health check. METHODS: The study population comprised 12,768 persons invited for a health check including...... screening for ischemic heart disease and lifestyle counseling. The study population was randomly drawn from a population of 179,097 persons living in 73 neighborhoods in Denmark. Data on neighborhood deprivation (percentage with basic education, with low income and not in work) and individual socioeconomic...

Differences in Fusarium Species in brown midrib Sorghum and in Air Populations in Production Fields.

Science.gov (United States)

Funnell-Harris, Deanna L; Scully, Erin D; Sattler, Scott E; French, Roy C; O'Neill, Patrick M; Pedersen, Jeffrey F

2017-11-01

Several Fusarium spp. cause sorghum (Sorghum bicolor) grain mold, resulting in deterioration and mycotoxin production in the field and during storage. Fungal isolates from the air (2005 to 2006) and from leaves and grain from wild-type and brown midrib (bmr)-6 and bmr12 plants (2002 to 2003) were collected from two locations. Compared with the wild type, bmr plants have reduced lignin content, altered cell wall composition, and different levels of phenolic intermediates. Multilocus maximum-likelihood analysis identified two Fusarium thapsinum operational taxonomic units (OTU). One was identified at greater frequency in grain and leaves of bmr and wild-type plants but was infrequently detected in air. Nine F. graminearum OTU were identified: one was detected at low levels in grain and leaves while the rest were only detected in air. Wright's F statistic (F ST ) indicated that Fusarium air populations differentiated between locations during crop anthesis but did not differ during vegetative growth, grain development, and maturity. F ST also indicated that Fusarium populations from wild-type grain were differentiated from those in bmr6 or bmr12 grain at one location but, at the second location, populations from wild-type and bmr6 grain were more similar. Thus, impairing monolignol biosynthesis substantially effected Fusarium populations but environment had a strong influence.

Phenotypic plasticity and population differentiation in an ongoing species invasion.

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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

DIFFERENTIATION OF BODY COMPOSITION OF PLAYERS OF THE POLISH NATIONAL BASEBALL TEAM

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Marina Jagiełło

2014-10-01

Full Text Available The purpose of the study is to identify the differentiation of body composition among players of Polish national baseball team in comparison to persons of the same population not professionally engaged in sport. The study involved Polish baseball representatives (n=20. Competitors’ age was 18-28 years, body mass from 67.7 kg to 114 kg (85±10.3 kg, and body height 173-196 cm (185.1±4.8. The training experience was 7-14 years and it was highly differentiated. The stoutness factor is the dominant factor among "infielders" and "pitchers", and among "outfielders" - the length one. The proportions of the features within the factors show that players are characterized by a strongly muscled forearm and a shank and by a clear predominance of the elbow width with a disproportionately - to the overall size of the factor - small knee and shoulder width. In the length factor an even contribution of the upper and lower extremity length with lower sitting body height can be noted. Depending on the position on the field there is a differentiation of the internal proportions of the body.

Controlling Population with Pollution

Science.gov (United States)

Browne, Joseph

2010-01-01

Population models are often discussed in algebra, calculus, and differential equations courses. In this article we will use the human population of the world as our application. After quick looks at two common models we'll investigate more deeply a model which incorporates the negative effect that accumulated pollution may have on population.

Human platelet lysate successfully promotes proliferation and subsequent chondrogenic differentiation of adipose-derived stem cells: a comparison with articular chondrocytes.

Science.gov (United States)

Hildner, F; Eder, M J; Hofer, K; Aberl, J; Redl, H; van Griensven, M; Gabriel, C; Peterbauer-Scherb, A

2015-07-01

Fetal calf serum (FCS) bears a potential risk for carrying diseases and eliciting immune reactions. Nevertheless, it still represents the gold standard as medium supplement in cell culture. In the present study, human platelet lysate (PL) was tested as an alternative to FCS for the expansion and subsequent chondrogenic differentiation of human adipose-derived stem cells (ASCs). ASCs were expanded with 10% FCS (group F) or 5% PL (group P). Subsequently, three-dimensional (3D) micromass pellets were created and cultured for 5 weeks in chondrogenic differentiation medium. Additionally, the de- and redifferentiation potential of human articular chondrocytes (HACs) was evaluated and compared to ASCs. Both HACs and ASCs cultured with PL showed strongly enhanced proliferation rates. Redifferentiation of HACs was possible for cells expanded up to 3.3 population doublings (PD). At this stage, PL-expanded HACs demonstrated better redifferentiation potential than FCS-expanded cells. ASCs could also be differentiated following extended passaging. Glycosaminoglycan (GAG) quantification and qRT-PCR of 10 cartilage related markers demonstrated a tendency for increased chondrogenic differentiation of PL-expanded ASCs compared to cells expanded with FCS. Histologically, collagen type II but also collagen type X was mainly present in group P. The present study demonstrates that PL strongly induces proliferation of ASCs, while the chondrogenic differentiation potential is retained. HACs also showed enhanced proliferation and even better redifferentiation when previously expanded with PL. This suggests that PL is superior to FCS as a supplement for the expansion of ASCs and HACs, particularly with regard to chondrogenic (re)differentiation. Copyright © 2013 John Wiley & Sons, Ltd.

Differential population synthesis of early-type galaxies. III. Synthesis results

International Nuclear Information System (INIS)

Pickles, A.J.

1985-01-01

Synthesis results are presented for 12 elliptical and five lenticular galaxies which cover nearly a 6 mag range of absolute magnitude in the Fornax cluster (V = 1430 km s -1 ). The results of age, metallicity, and mass-to-light ratio (M/L) determinations are presented differentially as functions of galactic luminosity and morphology. Bright elliptical galaxies are well represented by main-sequence turnoff colors of (V-R)/sub c/roughly-equal0.37 and B-Vroughly-equal0.70, in good agreement with O'Connell's results for bright Virgo ellipticals. The relatively young main-sequence turnoff ages, of 6-10 Gyr for ellipticals of all luminosities, indicate that substantial star formation activity occurred in these galaxies for a period of 6dagger10 Gyr after the epoch of globular cluster formation. There is strong evidence for small amounts of current star formation in at least the brightest ellipticals of all luminosities, indicate that substantial star formation in at least the brightest ellipticals, variation in the amount of which may account for significant dispersion in the cluster U-V versus V color-magnitude relation. A metallicity gradient in [Fe/H] of at least 0.16 dex per absolute magnitude is derived, with the brightest ellipticals being 2 to 3 times more metal-rich than solar. The mean metallicities and turnoff ages of the faintest ellipticals are probably dependent on environment. Distance-independent upper limits to galaxy M/L ratios derived from the syntheses conform well with M/L ratios derived from velocity dispersion measurements and give no evidence for unseen mass in the nuclei of early type galaxies of any luminosity

Strongly-correlated ultracold atoms in optical lattices

International Nuclear Information System (INIS)

Dao, Tung-Lam

2008-01-01

liquids, but also in unusual phases such as the normal state of high-temperature superconductivity with a pseudo gap (leading to a differentiation between nodes and anti-nodes) observed in condensed mater physics. In the second part of this thesis, we have performed theoretical studies of several phases of strongly correlated fermions in optical lattices in the framework of theoretical models such as the Hubbard model. We have implemented and developed analytical methods (Hartree-Fock mean field theory at weak coupling, mapping on a effective spin model at strong coupling) and numerical methods (the dynamic mean field theory approach). This work has led to two particular types of studies. The first one studies the competition between a superfluid phase and a density wave (or phase separation) for fermions with mass imbalance and attractive interaction. We have shown that the superfluid phase is unstable beyond a certain value of the mass ratio, which depends on the interaction. The second study treats a gas with imbalanced populations (polarized gas) with an attractive interaction in a three dimensional optical lattice. The main result is a phase diagram showing the stability of a uniform superfluid phase with polarization (Sarma phase or breached pair phase) in a certain parameter regime. Via an energetic argument, we concluded that the stability of the polarized superfluid phase is due to the reduction of the polarizability and the critical field of the non-polarized superfluid phase. In the strong coupling regime of the Hubbard model, within the DMFT method, we have shown that the formation of the preformed pair in the normal state reduces the polarizability and favors the stability of the breached pair phase. Although some aspects have been addressed in this thesis, many interesting questions still remain open for future work. In the first part, the framework of the novel spectroscopy method established in chapter 2 can allow for different concrete studies of the

The heterogeneous HLA genetic makeup of the Swiss population.

Science.gov (United States)

Buhler, Stéphane; Nunes, José Manuel; Nicoloso, Grazia; Tiercy, Jean-Marie; Sanchez-Mazas, Alicia

2012-01-01

This study aims at investigating the HLA molecular variation across Switzerland in order to determine possible regional differences, which would be highly relevant to several purposes: optimizing donor recruitment strategies in hematopoietic stem cell transplantation (HSCT), providing reliable reference data in HLA and disease association studies, and understanding the population genetic background(s) of this culturally heterogeneous country. HLA molecular data of more than 20,000 HSCT donors from 9-13 recruitment centers of the whole country were analyzed. Allele and haplotype frequencies were estimated by using new computer tools adapted to the heterogeneity and ambiguity of the data. Non-parametric and resampling statistical tests were performed to assess Hardy-Weinberg equilibrium, selective neutrality and linkage disequilibrium among different loci, both in each recruitment center and in the whole national registry. Genetic variation was explored through genetic distance and hierarchical analysis of variance taking into account both geographic and linguistic subdivisions in Switzerland. The results indicate a heterogeneous genetic makeup of the Swiss population: first, allele frequencies estimated on the whole national registry strongly deviate from Hardy-Weinberg equilibrium, by contrast with the results obtained for individual centers; second, a pronounced differentiation is observed for Ticino, Graubünden, and, to a lesser extent, Wallis, suggesting that the Alps represent(ed) a barrier to gene flow; finally, although cultural (linguistic) boundaries do not represent a main genetic differentiation factor in Switzerland, the genetic relatedness between population from south-eastern Switzerland and Italy agrees with historical and linguistic data. Overall, this study justifies the maintenance of a decentralized donor recruitment structure in Switzerland allowing increasing the genetic diversity of the national--and hence global--donor registry. It also

Significant genetic differentiation between native and introduced silver carp (Hypophthalmichthys molitrix) inferred from mtDNA analysis

Science.gov (United States)

Li, S.-F.; Xu, J.-W.; Yang, Q.-L.; Wang, C.H.; Chapman, D.C.; Lu, G.

2011-01-01

Silver carp Hypophthalmichthys molitrix (Cyprinidae) is native to China and has been introduced to over 80 countries. The extent of genetic diversity in introduced silver carp and the genetic divergence between introduced and native populations remain largely unknown. In this study, 241 silver carp sampled from three major native rivers and two non-native rivers (Mississippi River and Danube River) were analyzed using nucleotide sequences of mitochondrial COI gene and D-loop region. A total of 73 haplotypes were observed, with no haplotype found common to all the five populations and eight haplotypes shared by two to four populations. As compared with introduced populations, all native populations possess both higher haplotype diversity and higher nucleotide diversity, presumably a result of the founder effect. Significant genetic differentiation was revealed between native and introduced populations as well as among five sampled populations, suggesting strong selection pressures might have occurred in introduced populations. Collectively, this study not only provides baseline information for sustainable use of silver carp in their native country (i.e., China), but also offers first-hand genetic data for the control of silver carp in countries (e.g., the United States) where they are considered invasive.

Population-expression models of immune response

International Nuclear Information System (INIS)

Stromberg, Sean P; Antia, Rustom; Nemenman, Ilya

2013-01-01

The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenotype to an effector phenotype which controls the pathogen, and subsequently to a memory phenotype that is maintained and responsible for long-term protection. The expansion and the differentiation have been considered largely independently. Changes in cell populations are typically described using ecologically based ordinary differential equation models. In contrast, differentiation of single cells is studied within systems biology and is frequently modeled by considering changes in gene and protein expression in individual cells. Recent advances in experimental systems biology make available for the first time data to allow the coupling of population and high dimensional expression data of immune cells during infections. Here we describe and develop population-expression models which integrate these two processes into systems biology on the multicellular level. When translated into mathematical equations, these models result in non-conservative, non-local advection-diffusion equations. We describe situations where the population-expression approach can make correct inference from data while previous modeling approaches based on common simplifying assumptions would fail. We also explore how model reduction techniques can be used to build population-expression models, minimizing the complexity of the model while keeping the essential features of the system. While we consider problems in immunology in this paper, we expect population-expression models to be more broadly applicable. (paper)

INTERNAL-CYCLE VARIATION OF SOLAR DIFFERENTIAL ROTATION

International Nuclear Information System (INIS)

Li, K. J.; Xie, J. L.; Shi, X. J.

2013-01-01

The latitudinal distributions of the yearly mean rotation rates measured by Suzuki in 1998 and 2012 and Pulkkinen and Tuominen in 1998 are utilized to investigate internal-cycle variation of solar differential rotation. The rotation rate at the solar equator seems to have decreased since cycle 10 onward. The coefficient B of solar differential rotation, which represents the latitudinal gradient of rotation, is found to be smaller in the several years after the minimum of a solar cycle than in the several years after the maximum time of the cycle, and it peaks several years after the maximum time of the solar cycle. The internal-cycle variation of the solar rotation rates looks similar in profile to that of the coefficient B. A new explanation is proposed to address such a solar-cycle-related variation of the solar rotation rates. Weak magnetic fields may more effectively reflect differentiation at low latitudes with high rotation rates than at high latitudes with low rotation rates, and strong magnetic fields may more effectively repress differentiation at relatively low latitudes than at high latitudes. The internal-cycle variation is inferred as the result of both the latitudinal migration of the surface torsional pattern and the repression of strong magnetic activity in differentiation.

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

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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.

The population genetics of cultivation: domestication of a traditional Chinese medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae.

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Chuan Chen

Full Text Available BACKGROUND: Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement. RESULTS: Twenty-one cpDNA haplotypes of S. ningpoensis were identified. Wild populations contain all haplotypes, whereas only three haplotypes were found in cultivated populations with wild populations having twice the haplotype diversity of cultivated populations. Genetic differentiation between cultivated populations and wild populations was significant. Genomic AFLP markers revealed similar genetic diversity patterns. Furthermore, Structure analysis grouped all wild populations into two gene pools; two of which shared the same gene pool with cultivated S. ningpoensis. The result of Neighbor-Joining analysis was consistent with the structure analysis. In principal coordinate analysis, three cultivated populations from Zhejiang Province grouped together and were separated from other cultivated populations. CONCLUSIONS: These results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong

The population genetics of cultivation: domestication of a traditional Chinese medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae).

Science.gov (United States)

Chen, Chuan; Li, Pan; Wang, Rui-Hong; Schaal, Barbara A; Fu, Cheng-Xin

2014-01-01

Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement. Twenty-one cpDNA haplotypes of S. ningpoensis were identified. Wild populations contain all haplotypes, whereas only three haplotypes were found in cultivated populations with wild populations having twice the haplotype diversity of cultivated populations. Genetic differentiation between cultivated populations and wild populations was significant. Genomic AFLP markers revealed similar genetic diversity patterns. Furthermore, Structure analysis grouped all wild populations into two gene pools; two of which shared the same gene pool with cultivated S. ningpoensis. The result of Neighbor-Joining analysis was consistent with the structure analysis. In principal coordinate analysis, three cultivated populations from Zhejiang Province grouped together and were separated from other cultivated populations. These results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong artificial selection for medicinal quality has

Fortune favours the brave: Movement responses shape demographic dynamics in strongly competing populations.

Science.gov (United States)

Potts, Jonathan R; Petrovskii, Sergei V

2017-05-07

Animal movement is a key mechanism for shaping population dynamics. The effect of interactions between competing animals on a population's survival has been studied for many decades. However, interactions also affect an animal's subsequent movement decisions. Despite this, the indirect effect of these decisions on animal survival is much less well-understood. Here, we incorporate movement responses to foreign animals into a model of two competing populations, where inter-specific competition is greater than intra-specific competition. When movement is diffusive, the travelling wave moves from the stronger population to the weaker. However, by incorporating behaviourally induced directed movement towards the stronger population, the weaker one can slow the travelling wave down, even reversing its direction. Hence movement responses can switch the predictions of traditional mechanistic models. Furthermore, when environmental heterogeneity is combined with aggressive movement strategies, it is possible for spatially segregated co-existence to emerge. In this situation, the spatial patterns of the competing populations have the unusual feature that they are slightly out-of-phase with the environmental patterns. Finally, incorporating dynamic movement responses can also enable stable co-existence in a homogeneous environment, giving a new mechanism for spatially segregated co-existence. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

Science.gov (United States)

Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

2018-02-01

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

Resonance double magnetic bremsstrahlung in a strong magnetic field

International Nuclear Information System (INIS)

Fomin, P.I.; Kholodov, R.I.

2003-01-01

The possibility of resonance double magnetic bremsstrahlung in the approximation of weakly excited electron states in a strong external magnetic field is analyzed. The differential probability of this process in the Breit-Wigner form is obtained. The probability of double magnetic bremsstrahlung (second-order process of perturbation theory) is compared with the probability of magnetic bremsstrahlung (first-order process of perturbation theory)

The impact of divergence time on the nature of population structure: an example from Iceland.

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Alkes L Price

2009-06-01

Full Text Available The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs. We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.

Renormalisation of Nonequilibrium Phonons Under Strong Perturbative Influences.

Science.gov (United States)

Mehta, Sushrut Madhukar

Effects of strong perturbative influences, namely the presence of a narrow distribution of acoustic phonons, and the presence of an electron plasma, on the dynamics of nonequilibrium, near zone center, longitudinal optical phonons in GaP have been investigated in two separate experiments. The study of the effects of the interaction between the LO phonons and a heavily populated, narrow distribution of acoustic phonons lead to the observation of a new optically driven nonequilibrium phonon state. Time Resolved Coherent Antistokes Raman Scattering (TR-CARS), with picosecond resolution, was used to investigate the new mode. In order to achieve high occupation numbers in the acoustic branch, the picosecond laser pulses used were amplified up to 1.0 GW/cm^2 peak power per laser beam. An important characteristic property of the new state which differentiates it from the well known LO phonon state is the fact that rather than having the single decay rate observed under thermal equilibrium, the new state has two decay rates. Moreover, these two decay rates depend strongly on the distribution of the acoustic phonon occupation number. The coupling of the LO phonons with an electron plasma, on the other hand, was investigated by measurements of the shape of the Raman scattered line associated with the phonon-plasmon coupled mode. The plasma was generated by thermal excitation of carriers in doped samples. It was possible to study a large variety of plasma excitations by controlling the concentration of the dopant and the ambient temperature. A complete, self consistant model based on standard dielectric response theory is presented, and applied to the measurements of the phonon-plasmon coupled mode. It is possible to recover, via this model, the effective coupled mode damping rate, the plasma damping rate, and the plasma frequency as functions of ambient temperature, or the carrier concentration.

Complex postglacial recolonization inferred from population genetic structure of mottled sculpin Cottus bairdii in tributaries of eastern Lake Michigan, U.S.A.

Science.gov (United States)

Homola, J J; Ruetz, C R; Kohler, S L; Thum, R A

2016-11-01

This study used analyses of the genetic structure of a non-game fish species, the mottled sculpin Cottus bairdii to hypothesize probable recolonization routes used by cottids and possibly other Laurentian Great Lakes fishes following glacial recession. Based on samples from 16 small streams in five major Lake Michigan, U.S.A., tributary basins, significant interpopulation differentiation was documented (overall F ST = 0·235). Differentiation was complex, however, with unexpectedly high genetic similarity among basins as well as occasionally strong differentiation within basins, despite relatively close geographic proximity of populations. Genetic dissimilarities were identified between eastern and western populations within river basins, with similarities existing between eastern and western populations across basins. Given such patterns, recolonization is hypothesized to have occurred on three occasions from more than one glacial refugium, with a secondary vicariant event resulting from reduction in the water level of ancestral Lake Michigan. By studying the phylogeography of a small, non-game fish species, this study provides insight into recolonization dynamics of the region that could be difficult to infer from game species that are often broadly dispersed by humans. © 2016 The Fisheries Society of the British Isles.

High temperature increases the masculinization rate of the all-female (XX) rainbow trout "Mal" population.

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Valdivia, Karina; Jouanno, Elodie; Volff, Jean-Nicolas; Galiana-Arnoux, Delphine; Guyomard, René; Helary, Louise; Mourot, Brigitte; Fostier, Alexis; Quillet, Edwige; Guiguen, Yann

2014-01-01

Salmonids are generally considered to have a robust genetic sex determination system with a simple male heterogamety (XX/XY). However, spontaneous masculinization of XX females has been found in a rainbow trout population of gynogenetic doubled haploid individuals. The analysis of this masculinization phenotype transmission supported the hypothesis of the involvement of a recessive mutation (termed mal). As temperature effect on sex differentiation has been reported in some salmonid species, in this study we investigated in detail the potential implication of temperature on masculinization in this XX mal-carrying population. Seven families issued from XX mal-carrying parents were exposed from the time of hatching to different rearing water temperatures ((8, 12 and 18°C), and the resulting sex-ratios were confirmed by histological analysis of both gonads. Our results demonstrate that masculinization rates are strongly increased (up to nearly two fold) at the highest temperature treatment (18°C). Interestingly, we also found clear differences between temperatures on the masculinization of the left versus the right gonads with the right gonad consistently more often masculinized than the left one at lower temperatures (8 and 12°C). However, the masculinization rate is also strongly dependent on the genetic background of the XX mal-carrying families. Thus, masculinization in XX mal-carrying rainbow trout is potentially triggered by an interaction between the temperature treatment and a complex genetic background potentially involving some part of the genetic sex differentiation regulatory cascade along with some minor sex-influencing loci. These results indicate that despite its rather strict genetic sex determinism system, rainbow trout sex differentiation can be modulated by temperature, as described in many other fish species.

Characterisation of adaptive genetic diversity in environmentally contrasted populations of Eucalyptus camaldulensis Dehnh. (river red gum.

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Shannon Dillon

Full Text Available As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh. is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST = 17%, exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2 which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.

Genetic differentiation in natural populations of Lutzomyia longipalpis (Lutz & Neiva) (Diptera: Psychodidae) with different phenotypic spot patterns on tergites in males.

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Silva, M H; Nascimento, M D S B; Leonardo, F S; Rebêlo, J M M; Pereira, S R F

2011-01-01

Entomological surveys in the state of Maranhão have recorded morphologically distinct populations of Lutzomyia longipalpis (Lutz & Neiva). Some populations have one pair of spots (1S) on the fourth tergite, while others have two pairs (2S) on the third and fourth tergites of males. In the present study we investigated the degree of genetic polymorphism among four populations in the municipalities of Caxias, Codó and Raposa, in the state of Maranhão, Brazil, by using RAPD (Random Amplified Polymorphic DNA) markers. A total of 35 loci were identified, of which 30 were polymorphic. The highest polymorphism was observed with primer OPA 4, which produced 11 different profiles. Genetic diversity was assessed using grouping methods that produced a dendrogram in which the genotypes could be clearly separated into two main clades according to the number of spots on the male abdominal tergites. One cluster contained the populations from Caxias and Codó, and the other was formed by the populations from Raposa and Codó. The results of our RAPD analysis showed a clear separation between the populations with one and two pairs of spots. The epidemiologic significance of this genetic differentiation should be investigated in future studies.

Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

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Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

2015-01-01

Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers.

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Dong-Xiu Xue

Full Text Available The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure. Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene and current gene flow (through larval dispersal were responsible for the weak level of genetic structure detected in A. pectinata.

Solving SAT Problem Based on Hybrid Differential Evolution Algorithm

Science.gov (United States)

Liu, Kunqi; Zhang, Jingmin; Liu, Gang; Kang, Lishan

Satisfiability (SAT) problem is an NP-complete problem. Based on the analysis about it, SAT problem is translated equally into an optimization problem on the minimum of objective function. A hybrid differential evolution algorithm is proposed to solve the Satisfiability problem. It makes full use of strong local search capacity of hill-climbing algorithm and strong global search capability of differential evolution algorithm, which makes up their disadvantages, improves the efficiency of algorithm and avoids the stagnation phenomenon. The experiment results show that the hybrid algorithm is efficient in solving SAT problem.

Modeling and Prediction Using Stochastic Differential Equations

DEFF Research Database (Denmark)

Juhl, Rune; Møller, Jan Kloppenborg; Jørgensen, John Bagterp

2016-01-01

Pharmacokinetic/pharmakodynamic (PK/PD) modeling for a single subject is most often performed using nonlinear models based on deterministic ordinary differential equations (ODEs), and the variation between subjects in a population of subjects is described using a population (mixed effects) setup...... deterministic and can predict the future perfectly. A more realistic approach would be to allow for randomness in the model due to e.g., the model be too simple or errors in input. We describe a modeling and prediction setup which better reflects reality and suggests stochastic differential equations (SDEs...

Continuous strong Markov processes in dimension one a stochastic calculus approach

CERN Document Server

Assing, Sigurd

1998-01-01

The book presents an in-depth study of arbitrary one-dimensional continuous strong Markov processes using methods of stochastic calculus. Departing from the classical approaches, a unified investigation of regular as well as arbitrary non-regular diffusions is provided. A general construction method for such processes, based on a generalization of the concept of a perfect additive functional, is developed. The intrinsic decomposition of a continuous strong Markov semimartingale is discovered. The book also investigates relations to stochastic differential equations and fundamental examples of irregular diffusions.

Population Trends and the Status of Population Policy in Africa.

Science.gov (United States)

Rogge, John R.

1982-01-01

The major trend towards worldwide easing of the birthrate does not include the current population patterns in Africa. The population policies of African nations range along a continuum from totally pronatal to strongly antinatal. However, even antinatal policies have had little effect on the overall spiralling upward population trend. (JA)

Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

Science.gov (United States)

Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

2005-04-01

Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

Population Genetic Structure of Venturia effusa, Cause of Pecan Scab, in the Southeastern United States.

Science.gov (United States)

Bock, Clive H; Hotchkiss, Michael W; Young, Carolyn A; Charlton, Nikki D; Chakradhar, Mattupalli; Stevenson, Katherine L; Wood, Bruce W

2017-05-01

Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1). Clonality was low in all orchard populations (≤10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner's index = 3.49 to 4.59) and gene diversity (Nei's measure = 0.513 to 0.713). Analysis of molecular variance showed that, although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards and only 3% between trees within orchards. All populations could be differentiated from each other (P = 0.01), and various cluster analyses indicated that some populations were more closely related compared with other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern United States. Bayesian and nearest-neighbor methods suggested eight clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had pecan and pecan scab, which is that V. effusa became an issue on cultivated pecan in the last approximately 120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well

Differentiation analysis for estimating individual ancestry from the Tibetan Plateau by an archaic altitude adaptation EPAS1 haplotype among East Asian populations.

Science.gov (United States)

Jiang, Li; Peng, Jianxiong; Huang, Meisha; Liu, Jing; Wang, Ling; Ma, Quan; Zhao, Hui; Yang, Xin; Ji, Anquan; Li, Caixia

2018-02-10

Tibetans have adapted to the extreme environment of high altitude for hundreds of generations. A highly differentiated 5-SNP (Single Nucleotide Polymorphism) haplotype motif (AGGAA) on a hypoxic pathway gene, EPAS1, is observed in Tibetans and lowlanders. To evaluate the potential usage of the 5-SNP haplotype in ancestry inference for Tibetan or Tibetan-related populations, we analyzed this haplotype in 1053 individuals of 12 Chinese populations residing on the Tibetan Plateau, peripheral regions of Tibet, and plain regions. These data were integrated with the genotypes from the 1000 Genome populations and populations in a previously reported paper for population structure analyses. We found that populations representing highland and lowland groups have different dominant ancestry components. The core Denisovan haplotype (AGGAA) was observed at a frequency of 72.32% in the Tibetan Plateau, with a frequency range from 9.48 to 21.05% in the peripheral regions and Tibetan Plateau carried the archaic haplotype, while < 5% of the Chinese Han people carried the haplotype. Our findings indicate that the 5-SNP haplotype has a special distribution pattern in populations of Tibet and peripheral regions and could be integrated into AISNP (Ancestry Informative Single Nucleotide Polymorphism) panels to enhance ancestry resolution.

BMS-777607 promotes megakaryocytic differentiation and induces polyploidization in the CHRF-288-11 cells.

Science.gov (United States)

Nurhayati, Retno Wahyu; Ojima, Yoshihiro; Taya, Masahito

2015-04-01

Introduction of a polyploidy inducer is a promising strategy to achieve a high level of polyploidization during megakaryocytic (MK) differentiation. Here, we report that a multi-kinase inhibitor, BMS-777607, is a potent polyploidy inducer for elevating high ploidy cell formation in the MK-differentiated CHRF-288-11 (CHRF) cells. Our result showed that BMS-777607 strongly inhibited cell division without affecting cell viability when detected at day 1 after treatment. As a consequence, the high ploidy (≥8N) cells were accumulated in culture for 8 days, with an increase from 16.2 to 75.2 % of the total cell population. The elevated polyploidization was accompanied by the increased expression level of MK marker, CD41 (platelet glycoprotein IIb/IIIa, GPIIb/IIIa), suggesting that BMS-777607 promoted both polyploidization and commitment of MK-differentiated CHRF cells. Platelet-like fragments (PFs) were released by mature CHRF cells. Based on a flow cytometry assay, it was found that the PFs produced from BMS-777607-treated cells tended to have larger size and higher expression of GPIIb/IIIa, a receptor for platelet adhesion. Taken together, these results suggested that BMS-777607 promoted MK differentiation of CHRF cells and increased the functional property of platelet-like fragments.

The genetic structure of fermentative vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis.

Science.gov (United States)

Schuller, Dorit; Casal, Margarida

2007-02-01

From the analysis of six polymorphic microsatellite loci performed in 361 Saccharomyces cerevisiae isolates, 93 alleles were identified, 52 of them being described for the first time. All these isolates have a distinct mtDNA RFLP pattern. They are derived from a pool of 1620 isolates obtained from spontaneous fermentations of grapes collected in three vineyards of the Vinho Verde Region in Portugal, during the 2001-2003 harvest seasons. For all loci analyzed, observed heterozygosity was 3-4 times lower than the expected value supposing a Hardy-Weinberg equilibrium (random mating and no evolutionary mechanisms acting), indicating a clonal structure and strong populational substructuring. Genetic differences among S. cerevisiae populations were apparent mainly from gradations in allele frequencies rather than from distinctive "diagnostic" genotypes, and the accumulation of small allele-frequency differences across six loci allowed the identification of population structures. Genetic differentiation in the same vineyard in consecutive years was of the same order of magnitude as the differences verified among the different vineyards. Correlation of genetic differentiation with the distance between sampling points within a vineyard suggested a pattern of isolation-by-distance, where genetic divergence in a vineyard increased with size. The continuous use of commercial yeasts has a limited influence on the autochthonous fermentative yeast population collected from grapes and may just slightly change populational structures of strains isolated from sites very close to the winery where they have been used. The present work is the first large-scale approach using microsatellite typing allowing a very fine resolution of indigenous S. cerevisiae populations isolated from vineyards.

Methodological approach for substantiating disease freedom in a heterogeneous small population. Application to ovine scrapie, a disease with a strong genetic susceptibility.

Science.gov (United States)

Martinez, Marie-José; Durand, Benoit; Calavas, Didier; Ducrot, Christian

2010-06-01

Demonstrating disease freedom is becoming important in different fields including animal disease control. Most methods consider sampling only from a homogeneous population in which each animal has the same probability of becoming infected. In this paper, we propose a new methodology to calculate the probability of detecting the disease if it is present in a heterogeneous population of small size with potentially different risk groups, differences in risk being defined using relative risks. To calculate this probability, for each possible arrangement of the infected animals in the different groups, the probability that all the animals tested are test-negative given this arrangement is multiplied by the probability that this arrangement occurs. The probability formula is developed using the assumption of a perfect test and hypergeometric sampling for finite small size populations. The methodology is applied to scrapie, a disease affecting small ruminants and characterized in sheep by a strong genetic susceptibility defining different risk groups. It illustrates that the genotypes of the tested animals influence heavily the confidence level of detecting scrapie. The results present the statistical power for substantiating disease freedom in a small heterogeneous population as a function of the design prevalence, the structure of the sample tested, the structure of the herd and the associated relative risks. (c) 2010 Elsevier B.V. All rights reserved.

Mesenchymal stem cell proliferation and mineralization but not osteogenic differentiation are strongly affected by extracellular pH.

Science.gov (United States)

Fliefel, Riham; Popov, Cvetan; Tröltzsch, Matthias; Kühnisch, Jan; Ehrenfeld, Michael; Otto, Sven

2016-06-01

Osteomyelitis is a serious complication in oral and maxillofacial surgery affecting bone healing. Bone remodeling is not only controlled by cellular components but also by ionic and molecular composition of the extracellular fluids in which calcium phosphate salts are precipitated in a pH dependent manner. To determine the effect of pH on self-renewal, osteogenic differentiation and matrix mineralization of mesenchymal stem cells (MSCs). We selected three different pH values; acidic (6.3, 6.7), physiological (7.0-8.0) and severe alkaline (8.5). MSCs were cultured at different pH ranges, cell viability measured by WST-1, apoptosis detected by JC-1, senescence was analyzed by β-galactosidase whereas mineralization was detected by Alizarin Red and osteogenic differentiation analyzed by Real-time PCR. Self-renewal was affected by pH as well as matrix mineralization in which pH other than physiologic inhibited the deposition of extracellular matrix but did not affect MSCs differentiation as osteoblast markers were upregulated. The expression of osteocalcin and alkaline phosphatase activity was upregulated whereas osteopontin was downregulated under acidic pH. pH affected MSCs self-renewal and mineralization without influencing osteogenic differentiation. Thus, future therapies, based on shifting acid-base balance toward the alkaline direction might be beneficial for prevention or treatment of osteomyelitis. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

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

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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.

Trait differences in responses to arbuscular mycorrhizal fungi are stronger and more consistent than fixed differences among populations of Asclepias speciosa.

Science.gov (United States)

Waller, Lauren P; Hahn, Philip G; Maron, John L; Lekberg, Ylva

2018-02-01

Arbuscular mycorrhizal (AM) fungi can promote plant growth and reproduction, but other plant physiological traits or traits that provide defense against herbivores can also be affected by AM fungi. However, whether responses of different traits to AM fungi are correlated and whether these relationships vary among plants from different populations are unresolved. In a common garden experiment, we grew Asclepias speciosa plants from seed collected from populations found along an environmental gradient with and without AM fungi to assess whether the responses of six growth and defense traits to AM fungi are correlated. Although there was strong genetic differentiation in mean trait values among populations, AM fungi consistently increased expression of most growth and defense traits across all populations. Responses of biomass and root to shoot ratio to AM fungi were positively correlated, suggesting that plants that are more responsive to AM fungi allocated more biomass belowground. Responses of biomass and trichome density to AM fungi were negatively correlated, indicating a trade-off in responsiveness between a growth and defensive trait. Our results suggest that while there is substantial population differentiation in many traits of A. speciosa, populations respond similarly to AM fungi, and both positive and negative correlations among trait responses occur. © 2018 Botanical Society of America.

Population structure and genetic variability of mainland and insular populations of the Neotropical water rat, Nectomys squamipes (Rodentia, Sigmodontinae

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Francisca C. Almeida

2005-12-01

Full Text Available Seven microsatellite loci were used to investigate the genetic variability and structure of six mainland and two island populations of the Neotropical water rat Nectomys squamipes, a South American semi-aquatic rodent species with a wide distribution. High levels of variability were found within mainland populations while island populations were less variable but the more differentiated in respect to allele number and frequency. The time of biological divergence between mainland and island populations coincided with geological data. A significant geographic structure was found in mainland populations (theta = 0.099; rho = 0.086 although the degree of differentiation was relatively low in respect to the distance between surveyed localities (24 to 740 km. Genetic and geographic distances were not positively correlated as previously found with random amplified polymorphic DNA (RAPD markers. Significant but low genetic differentiation in the mainland and lack of isolation by distance can be explained by large population size and/or recent population expansion. Additionally, the agreement between the age of geologic events (sea level fluctuations and divergence times for insular populations points to a good reference for molecular clock calibration to associate recent environmental changes and the distribution pattern of small mammals in the Brazilian Atlantic Forest.

Worldwide variation in hip fracture incidence weakly aligns with genetic divergence between populations.

Science.gov (United States)

Wallace, I J; Botigué, L R; Lin, M; Smaers, J B; Henn, B M; Grine, F E

2016-09-01

This study investigates the influence of genetic differentiation in determining worldwide heterogeneity in osteoporosis-related hip fracture rates. The results indicate that global variation in fracture incidence exceeds that expected on the basis of random genetic variance. Worldwide, the incidence of osteoporotic hip fractures varies considerably. This variability is believed to relate mainly to non-genetic factors. It is conceivable, however, that genetic susceptibility indeed differs across populations. Here, we present the first quantitative assessment of the effects of genetic differentiation on global variability in hip fracture rates. We investigate the observed variance in publically reported age-standardized rates of hip fracture among 28 populations from around the world relative to the expected variance given the phylogenetic relatedness of these populations. The extent to which these variances are similar constitutes a "phylogenetic signal," which was measured using the K statistic. Population genetic divergence was calculated using a robust array of genome-wide single nucleotide polymorphisms. While phylogenetic signal is maximized when K > 1, a K value of only 0.103 was detected in the combined-sex fracture rate pattern across the 28 populations, indicating that fracture rates vary more than expected based on phylogenetic relationships. When fracture rates for the sexes were analyzed separately, the degree of phylogenetic signal was also found to be small (females: K = 0.102; males: K = 0.081). The lack of a strong phylogenetic signal underscores the importance of factors other than stochastic genetic diversity in shaping worldwide heterogeneity in hip fracture incidence.

HOX and TALE signatures specify human stromal stem cell populations from different sources.

Science.gov (United States)

Picchi, Jacopo; Trombi, Luisa; Spugnesi, Laura; Barachini, Serena; Maroni, Giorgia; Brodano, Giovanni Barbanti; Boriani, Stefano; Valtieri, Mauro; Petrini, Mario; Magli, Maria Cristina

2013-04-01

Human stromal stem cell populations reside in different tissues and anatomical sites, however a critical question related to their efficient use in regenerative medicine is whether they exhibit equivalent biological properties. Here, we compared cellular and molecular characteristics of stromal stem cells derived from the bone marrow, at different body sites (iliac crest, sternum, and vertebrae) and other tissues (dental pulp and colon). In particular, we investigated whether homeobox genes of the HOX and TALE subfamilies might provide suitable markers to identify distinct stromal cell populations, as HOX proteins control cell positional identity and, together with their co-factors TALE, are involved in orchestrating differentiation of adult tissues. Our results show that stromal populations from different sources, although immunophenotypically similar, display distinct HOX and TALE signatures, as well as different growth and differentiation abilities. Stromal stem cells from different tissues are characterized by specific HOX profiles, differing in the number and type of active genes, as well as in their level of expression. Conversely, bone marrow-derived cell populations can be essentially distinguished for the expression levels of specific HOX members, strongly suggesting that quantitative differences in HOX activity may be crucial. Taken together, our data indicate that the HOX and TALE profiles provide positional, embryological and hierarchical identity of human stromal stem cells. Furthermore, our data suggest that cell populations derived from different body sites may not represent equivalent cell sources for cell-based therapeutical strategies for regeneration and repair of specific tissues. Copyright © 2012 Wiley Periodicals, Inc.

Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids.

Science.gov (United States)

Peris, David; Sylvester, Kayla; Libkind, Diego; Gonçalves, Paula; Sampaio, José Paulo; Alexander, William G; Hittinger, Chris Todd

2014-04-01

Reticulate evolution can be a major driver of diversification into new niches, especially in disturbed habitats and at the edges of ranges. Industrial fermentation strains of yeast provide a window into these processes, but progress has been hampered by a limited understanding of the natural diversity and distribution of Saccharomyces species and populations. For example, lager beer is brewed with Saccharomyces pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a species only recently discovered in Patagonia, Argentina. Here, we report that genetically diverse strains of S. eubayanus are readily isolated from Patagonia, demonstrating that the species is well established there. Analyses of multilocus sequence data strongly suggest that there are two diverse and highly differentiated Patagonian populations. The low nucleotide diversity found in the S. eubayanus moiety of hybrid European brewing strains suggests that their alleles were drawn from a small subpopulation that is closely related to one of the Patagonian populations. For the first time, we also report the rare isolation of S. eubayanus outside Patagonia, in Wisconsin, USA. In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. These complex and varied reticulation events are not adequately captured by conventional phylogenetic methods and required analyses of Bayesian concordance factors and phylogenetic networks to accurately summarize and interpret. These findings show how genetically diverse eukaryotic microbes can produce rare but economically important hybrids with low genetic diversity when they migrate from their natural ecological context. © 2014 John Wiley & Sons Ltd.

Assessing the impact of stocking northern-origin hatchery brook trout on the genetics of wild populations in North Carolina

Science.gov (United States)

Kazyak, David C.; Rash, Jacob; Lubinski, Barbara A.; King, Tim L.

2018-01-01

The release of hatchery-origin fish into streams with endemics can degrade the genetics of wild populations if interbreeding occurs. Starting in the 1800s, brook trout descendent from wild populations in the northeastern United States were stocked from hatcheries into streams across broad areas of North America to create and enhance fishery resources. Across the southeastern United States, many millions of hatchery-origin brook trout have been released into hundreds of streams, but the extent of introgression with native populations is not well resolved despite large phylogeographic distances between these groups. We used three assessment approaches based on 12 microsatellite loci to examine the extent of hatchery introgression in 406 wild brook trout populations in North Carolina. We found high levels of differentiation among most collections (mean F′ST = 0.718), and among most wild collections and hatchery strains (mean F′ST = 0.732). Our assessment of hatchery introgression was consistent across the three metrics, and indicated that most wild populations have not been strongly influenced by supplemental stocking. However, a small proportion of wild populations in North Carolina appear to have been strongly influenced by stocked conspecifics, or in some cases, may have been founded entirely by hatchery lineages. In addition, we found significant differences in the apparent extent of hatchery introgression among major watersheds, with the Savannah River being the most strongly impacted. Conversely, populations in the Pee Dee River watershed showed little to no evidence of hatchery introgression. Our study represents the first large-scale effort to quantify the extent of hatchery introgression across brook trout populations in the southern Appalachians using highly polymorphic microsatellite markers.

Multiple populations of pantropical spotted dolphins in Hawaiian waters.

Science.gov (United States)

Courbis, Sarah; Baird, Robin W; Cipriano, Frank; Duffield, Deborah

2014-01-01

Understanding gene flow and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on animal populations. In Hawaii, most species of odontocetes are managed as single populations. Recent exceptions include false killer whales, spinner dolphins, and common bottlenose dolphins, for which studies have shown fidelity to individual islands or groups of islands. Our study focused on pantropical spotted dolphins. We analyzed mitochondrial control region and 11 microsatellite loci from 101 individuals from 4 areas: Hawaii, Maui/Lanai, Oahu, and Kauai/Niihau. We examined F ST, F' ST, R ST, Jost's D, and ΦST and used TESS to estimate number of populations and assignment probabilities. Our results support genetic differentiation among Hawaii, Maui/Lanai, and Oahu and suggest that pantropical spotted dolphins near Kauai/Niihau are likely transient and in low numbers. Between island regions, F ST for microsatellites ranged from 0.016 to 0.045 and for mtDNA, from 0.011 to 0.282. F ' ST, ranged from 0.098 to 0.262 for microsatellites and 0.019 to 0.415 for mtDNA. R ST and ΦST showed similar results to F ST for microsatellites and mtDNA respectively, and Jost's D fell between F ST and F ' ST. TESS supported 3 populations, and greatest mean assignment probability by island region ranged from 0.50 to 0.72. The private alleles method indicated migration rates among regions from 1.49 to 3.45, and effective population size of the island of Hawaii was estimated to be 220. There was no strong evidence to support sex-biased dispersal or group fidelity. Considering this study in the larger context of other odontocete population studies and studies of connectivity, we suggest genetic differentiation may be mediated by behavior adapted to differing habitat types and niches. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A cell population that strongly expresses the CB1 cannabinoid receptor in the ependyma of the rat spinal cord.

Science.gov (United States)

Garcia-Ovejero, Daniel; Arevalo-Martin, Angel; Paniagua-Torija, Beatriz; Sierra-Palomares, Yolanda; Molina-Holgado, Eduardo

2013-01-01

The cells surrounding the central canal of the spinal cord are a source of stem/precursor cells that may give rise to neurons, astrocytes, or oligodendrocytes. However, they are a heterogeneous population that remains poorly understood. Here we describe a subpopulation characterized by their strong expression of the CB(1) cannabinoid receptor, oval/round soma, apical nucleus, a variable number of cilia (0, 1, or 2), and the presence of a single short and occasionally ramified basal process. These cells are mainly located in the lateral and dorsal central canal throughout the spinal cord. These CB(1)(HIGH) cells are closely related to the basal lamina labyrinths or fractones derived from subependymal microglia. In addition, CB(1)(HIGH) cells express some stem/precursor cell markers, including vimentin, nestin, Sox2, Sox9, and GLAST, but not others such as CD15 or GFAP. In addition, this cell population does not proliferate in the intact adult spinal cord, although up to 50% of these cells express the proliferation marker Ki67 in newly born rats or after a spinal cord contusion. The present findings contribute to our understanding of the spinal cord central canal structure and reveal the targets for endocannabinoids inside this neurogenic niche. Copyright © 2012 Wiley Periodicals, Inc.

Strong and Electromagnetic Interactions at SPS Energies

CERN Document Server

Ribicki, Andrzej

2009-01-01

Particle production in peripheral Pb+Pb collisions has been measured at a beam energy of 158 GeV per nucleon, corresponding to psNN 17.3 GeV. The measurements provide full double differential coverage in a wide range of longitudinal and transverse momenta, including the central (“mid-rapidity”) area and extending far into the projectile fragmentation region. The resulting analysis shows the heavy ion reaction as a mixture of different processes. In particular, surprising phenomena, like the presence of large and strongly varying structures in the shape of the double differential cross section d2s /dxFd pT , are induced by the final state electromagnetic interaction between produced particles and the charged spectator system. This effect is largest at low transverse momenta, where it results in a deep valley in the xF -dependence of the produced p+/p− ratio. The basic characteristics of the electromagnetic phenomenon described above agree with the results of a theoretical analysis, performed by means of ...

On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions.

Science.gov (United States)

Gerencsér, Máté; Jentzen, Arnulf; Salimova, Diyora

2017-11-01

In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14 , 1477-1500 (doi:10.4310/CMS.2016.v14.n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ∈{4,5,…}, there exist d -dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two ( d =2) and three ( d =3) space dimensions.

Population genetics of Manihot esculenta ssp. flabellifolia gives insight into past distribution of xeric vegetation in a postulated forest refugium area in northern Amazonia.

Science.gov (United States)

Duputié, Anne; Delêtre, Marc; De Granville, Jean-Jacques; McKey, Doyle

2009-07-01

The Guianas have often been proposed as a forest refugium; however, this view has received little testing. Studies of population genetics of forest taxa suggest that the central part of French Guiana remained forested, while the southern part (currently forested) may have harboured more open vegetation. Insights into the population structure of species restricted to non-forested habitats can help test this hypothesis. Using six microsatellite loci, we investigated the population genetics of French Guianan accessions of Manihot esculenta ssp. flabellifolia, a taxon restricted to coastal savannas and to rocky outcrops in the densely forested inland. Coastal populations were highly differentiated from one another, and our data suggest a recent colonization of these savannas by M. esculenta ssp. flabellifolia in a west-to-east process. Coastal populations were strongly differentiated from inselberg populations, consistent with an ancient separation of these two groups, with no or low subsequent gene flow. This supports the hypothesis that the central part of the region may have remained forested since the Last Glacial Maximum, impeding the establishment of Manihot. Contrary to coastal populations, inselberg Manihot populations were strikingly homogeneous at a broad spatial scale. This suggests they were connected until recently, either by a large continuous savanna area or by smaller, temporary disturbed areas shifting in space.

Genetic structure of populations and differentiation in forest trees

Science.gov (United States)

Raymond P. Guries; F. Thomas Ledig

1981-01-01

Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog (Rana temporaria?

Directory of Open Access Journals (Sweden)

Patrick P. Lenhardt

2017-07-01

Full Text Available Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria populations in Southern Palatinate (Germany. We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance. Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat

Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population.

Science.gov (United States)

Nakaoka, Hirofumi; Mitsunaga, Shigeki; Hosomichi, Kazuyoshi; Shyh-Yuh, Liou; Sawamoto, Taiji; Fujiwara, Tsutomu; Tsutsui, Naohisa; Suematsu, Koji; Shinagawa, Akira; Inoko, Hidetoshi; Inoue, Ituro

2013-01-01

The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.

Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

DEFF Research Database (Denmark)

Kim, Yung Hae; Larsen, Hjalte List; Rué, Paul

2015-01-01

Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine...

Impulsive differential inclusions a fixed point approach

CERN Document Server

Ouahab, Abdelghani; Henderson, Johnny

2013-01-01

Impulsive differential equations have been developed in modeling impulsive problems in physics, population dynamics, ecology, biotechnology, industrial robotics, pharmacokinetics, optimal control, etc. The questions of existence and stability of solutions for different classes of initial values problems for impulsive differential equations and inclusions with fixed and variable moments are considered in detail. Attention is also given to boundary value problems and relative questions concerning differential equations. This monograph addresses a variety of side issues that arise from its simple

Differentiation of breast cancer stem cells by knockdown of CD44: promising differentiation therapy

Directory of Open Access Journals (Sweden)

Pham Phuc V

2011-12-01

Full Text Available Abstract Background Breast cancer stem cells (BCSCs are the source of breast tumors. Compared with other cancer cells, cancer stem cells show high resistance to both chemotherapy and radiotherapy. Targeting of BCSCs is thus a potentially promising and effective strategy for breast cancer treatment. Differentiation therapy represents one type of cancer stem-cell-targeting therapy, aimed at attacking the stemness of cancer stem cells, thus reducing their chemo- and radioresistance. In a previous study, we showed that down-regulation of CD44 sensitized BCSCs to the anti-tumor agent doxorubicin. This study aimed to determine if CD44 knockdown caused BCSCs to differentiate into breast cancer non-stem cells (non-BCSCs. Methods We isolated a breast cancer cell population (CD44+CD24- cells from primary cultures of malignant breast tumors. These cells were sorted into four sub-populations based on their expression of CD44 and CD24 surface markers. CD44 knockdown in the BCSC population was achieved using small hairpin RNA lentivirus particles. The differentiated status of CD44 knock-down BCSCs was evaluated on the basis of changes in CD44+CD24- phenotype, tumorigenesis in NOD/SCID mice, and gene expression in relation to renewal status, metastasis, and cell cycle in comparison with BCSCs and non-BCSCs. Results Knockdown of CD44 caused BCSCs to differentiate into non-BCSCs with lower tumorigenic potential, and altered the cell cycle and expression profiles of some stem cell-related genes, making them more similar to those seen in non-BCSCs. Conclusions Knockdown of CD44 is an effective strategy for attacking the stemness of BCSCs, resulting in a loss of stemness and an increase in susceptibility to chemotherapy or radiation. The results of this study highlight a potential new strategy for breast cancer treatment through the targeting of BCSCs.

Investigating population differentiation in a major African agricultural pest: evidence from geometric morphometrics and connectivity suggests high invasion potential.

Science.gov (United States)

Karsten, M; Addison, P; Jansen van Vuuren, B; Terblanche, J S

2016-07-01

The distribution, spatial pattern and population dynamics of a species can be influenced by differences in the environment across its range. Spatial variation in climatic conditions can cause local populations to undergo disruptive selection and ultimately result in local adaptation. However, local adaptation can be constrained by gene flow and may favour resident individuals over migrants-both are factors critical to the assessment of invasion potential. The Natal fruit fly (Ceratitis rosa) is a major agricultural pest in Africa with a history of island invasions, although its range is largely restricted to south east Africa. Across Africa, C. rosa is genetically structured into two clusters (R1 and R2), with these clusters occurring sympatrically in the north of South Africa. The spatial distribution of these genotypic clusters remains unexamined despite their importance for understanding the pest's invasion potential. Here, C. rosa, sampled from 22 South African locations, were genotyped at 11 polymorphic microsatellite loci and assessed morphologically using geometric morphometric wing shape analyses to investigate patterns of population structure and determine connectedness of pest-occupied sites. Our results show little to no intraspecific (population) differentiation, high population connectivity, high effective population sizes and only one morphological type (R2) within South Africa. The absence of the R1 morphotype at sites where it was previously found may be a consequence of differences in thermal niches of the two morphotypes. Overall, our results suggest high invasion potential of this species, that area-wide pest management should be undertaken on a country-wide scale, and that border control is critical to preventing further invasions. © 2016 John Wiley & Sons Ltd.

A generalization of the virial theorem for strongly singular potentials

International Nuclear Information System (INIS)

Gesztesy, F.; Pittner, L.

1978-09-01

Using scale transformations the authors prove a generalization of the virial theorem for the eigenfunctions of non-relativistic Schroedinger Hamiltonians which are defined as the Friedrichs extension of strongly singular differential operators. The theorem also applies to situations where the ground state has divergent kinetic and potential energy and thus the usual version of the virial theorem becomes meaningless. (Auth.)

Distance, dams and drift: What structures populations of an endangered, benthic stream fish?

Science.gov (United States)

Roberts, James H.; Angermeier, Paul; Hallerman, Eric M.

2013-01-01

Spatial population structure plays an important role in species persistence, evolution and conservation. Benthic stream fishes are diverse and frequently imperilled, yet the determinants and spatial scaling of their population structure are understudied. We investigated the range-wide population genetic structure of Roanoke logperch (Percina rex), an endangered, benthic stream fish of the eastern United States. Fish were sampled from 35 sites and analysed at 11 microsatellite DNA loci. Clustering models were used to sort individuals into genetically cohesive groups and thereby estimate the spatial scaling of population structure. We then used Bayesian generalized linear mixed models (BGLMMs) to test alternative hypotheses about the environmental factors most responsible for generating structure, as measured by the differentiation statistic FST. Clustering models delineated seven discrete populations, whose boundaries coincided with agents of fragmentation, including hydroelectric dams and tailwaters. In the absence of hydrological barriers, gene flow was extensive throughout catchments, whereas there was no evidence for contemporary dispersal between catchments across barriers. In the best-supported BGLMM, FST was positively related to the spatial distance and degree of hydrological alteration between sites and negatively related to genetic diversity within sites. Whereas the effect of tailwaters was equivocal, dams strongly influenced differentiation: the effect of a dam on FST was comparable to that of a between-site distance of over 1200 km of unimpounded river. Overall, the effect of distance-mediated dispersal was negligible compared to the combined effects of fragmentation and genetic drift. The contemporary population structure of P. rex comprises a few geographically extensive ‘islands’ that are fragmented by hydroelectric projects. This information clarifies the importance of a catchment-scale perspective on conserving the species and

Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.

Science.gov (United States)

Jueterbock, A; Franssen, S U; Bergmann, N; Gu, J; Coyer, J A; Reusch, T B H; Bornberg-Bauer, E; Olsen, J L

2016-11-01

Populations distributed across a broad thermal cline are instrumental in addressing adaptation to increasing temperatures under global warming. Using a space-for-time substitution design, we tested for parallel adaptation to warm temperatures along two independent thermal clines in Zostera marina, the most widely distributed seagrass in the temperate Northern Hemisphere. A North-South pair of populations was sampled along the European and North American coasts and exposed to a simulated heatwave in a common-garden mesocosm. Transcriptomic responses under control, heat stress and recovery were recorded in 99 RNAseq libraries with ~13 000 uniquely annotated, expressed genes. We corrected for phylogenetic differentiation among populations to discriminate neutral from adaptive differentiation. The two southern populations recovered faster from heat stress and showed parallel transcriptomic differentiation, as compared with northern populations. Among 2389 differentially expressed genes, 21 exceeded neutral expectations and were likely involved in parallel adaptation to warm temperatures. However, the strongest differentiation following phylogenetic correction was between the three Atlantic populations and the Mediterranean population with 128 of 4711 differentially expressed genes exceeding neutral expectations. Although adaptation to warm temperatures is expected to reduce sensitivity to heatwaves, the continued resistance of seagrass to further anthropogenic stresses may be impaired by heat-induced downregulation of genes related to photosynthesis, pathogen defence and stress tolerance. © 2016 John Wiley & Sons Ltd.

Strong drifts effects on neoclassical transport

International Nuclear Information System (INIS)

Tessarotto, M.; Gregoratto, D.; White, R.B.

1996-01-01

It is well known that strong drifts play an important role in plasma equilibrium, stability and confinement A significant example concerns, in particular for tokamak plasmas, the case of strong toroidal differential rotation produced by E x B drift which is currently regarded as potentially important for its influence in equilibrium, stability and transport. In fact, theoretically, it has been found that shear flow can substantially affect the stability of microinstabilities as well modify substantially transport. Recent experimental observations of enhanced confinement and transport regimes in Tokamaks, show, however, evidence of the existence of strong drifts in the plasma core. These are produced not only by the radial electric field [which gives rise to the E x B drift], but also by density [N s ], temperature [T s ] and mass flow [V = ωRe var-phi , with e var-phi the toroidal unit vector, R the distance for the symmetry axis of the torus and ω being the toroidal angular rotation velocity] profiles which are suitably steep. This implies that, in a significant part of the plasma core, the relevant scale lengths of the gradients [of N s , T s , ω], i.e., respectively L N , L T and L ω can be as large as the radial scale length characterizing the banana orbits, L b . Interestingly enough, the transport estimates obtained appear close or even lower than the predictions based on the simplest neoclassical model. However, as is well known, the latter applies, in a strict sense only in the case of weak drifts and also ignoring even the contribution of shear flow related to strong E x B drift. Thus a fundamental problem appears the extension of neoclassical transport theory to include the effect of strong drifts in Tokamak confinement systems. The goal of this investigation is to develop a general formulation of neoclassical transport embodying such important feature

Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1

Science.gov (United States)

Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A.; Schönian, Gabriele

2008-01-01

Background 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. Methodology/Principal Findings 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. Conclusion 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

Precision determination of the strong coupling constant within a global PDF analysis

NARCIS (Netherlands)

Ball, Richard D.; Carrazza, Stefano; Debbio, Luigi Del; Forte, Stefano; Kassabov, Zahari; Rojo, Juan; Slade, Emma; Ubiali, Maria

2018-01-01

We present a determination of the strong coupling constant $\\alpha_s(m_Z)$ based on the NNPDF3.1 determination of parton distributions, which for the first time includes constraints from jet production, top-quark pair differential distributions, and the $Z$ $p_T$ distributions using exact NNLO

Advanced differential quadrature methods

CERN Document Server

Zong, Zhi

2009-01-01

Modern Tools to Perform Numerical DifferentiationThe original direct differential quadrature (DQ) method has been known to fail for problems with strong nonlinearity and material discontinuity as well as for problems involving singularity, irregularity, and multiple scales. But now researchers in applied mathematics, computational mechanics, and engineering have developed a range of innovative DQ-based methods to overcome these shortcomings. Advanced Differential Quadrature Methods explores new DQ methods and uses these methods to solve problems beyond the capabilities of the direct DQ method.After a basic introduction to the direct DQ method, the book presents a number of DQ methods, including complex DQ, triangular DQ, multi-scale DQ, variable order DQ, multi-domain DQ, and localized DQ. It also provides a mathematical compendium that summarizes Gauss elimination, the Runge-Kutta method, complex analysis, and more. The final chapter contains three codes written in the FORTRAN language, enabling readers to q...

India's population: second and growing.

Science.gov (United States)

Visaria, P; Visaria, L

1981-10-01

Attention in this discussion of the population of India is directed to the following: international comparisons, population pressures, trends in population growth (interstate variations), sex ratio and literacy, urban-rural distribution, migration (interstate migration, international migration), fertility and mortality levels, fertility trends (birth rate decline, interstate fertility differentials, rural-urban fertility decline, fertility differentials by education and religion, marriage and fertility), mortality trends (mortality differentials, health care services), population pressures on socioeconomic development (per capita income and poverty, unemployment and employment, increasing foodgrain production, school enrollment shortfalls), the family planning program, implementing population policy statements, what actions would be effective, and goals and prospects for the future. India's population, a total of 684 million persons as of March 1, 1981, is 2nd only to the population of China. The 1981 population was up by 136 million persons, or 24.75%, over the 548 million enumerated in the 1971 census. For 1978, India's birth and death rates were estimated at 33.3 and 14.2/1000 population, down from about 41.1 and 18.9 during the mid-1960s. India's current 5-year plan has set a goal of a birth rate of 30/1000 population by 1985 and "replacement-level" fertility--about 2.3 births per woman--by 1996. The acceleration in India's population growth has come mainly in the past 3 decades and is due primarily to a decline in mortality that has markedly outstripped the fertility decline. The Janata Party which assumed government leadership in March 1977 did not dismantle the family planning program, but emphasis was shifted to promote family planning "without any compulsion, coercion or pressures of any sort." The policy statement stressed that efforts were to be directed towards those currently underserved, mainly in rural areas. Hard targets were rejected. Over the 1978

Morpho-phenological diversity among natural populations of ...

African Journals Online (AJOL)

... the high levels of within population variation and the lack of correlation between population differentiation and geographical distances suggest a potentially important rate of long-distance seed dispersal and confirm the role played by natural selection in the population structure of Tunisian populations of M. polymorpha.

Prion protein expression regulates embryonic stem cell pluripotency and differentiation.

Directory of Open Access Journals (Sweden)

Alberto Miranda

2011-04-01

Full Text Available Cellular prion protein (PRNP is a glycoprotein involved in the pathogenesis of transmissible spongiform encephalopathies (TSEs. Although the physiological function of PRNP is largely unknown, its key role in prion infection has been extensively documented. This study examines the functionality of PRNP during the course of embryoid body (EB differentiation in mouse Prnp-null (KO and WT embryonic stem cell (ESC lines. The first feature observed was a new population of EBs that only appeared in the KO line after 5 days of differentiation. These EBs were characterized by their expression of several primordial germ cell (PGC markers until Day 13. In a comparative mRNA expression analysis of genes playing an important developmental role during ESC differentiation to EBs, Prnp was found to participate in the transcription of a key pluripotency marker such as Nanog. A clear switching off of this gene on Day 5 was observed in the KO line as opposed to the WT line, in which maximum Prnp and Nanog mRNA levels appeared at this time. Using a specific antibody against PRNP to block PRNP pathways, reduced Nanog expression was confirmed in the WT line. In addition, antibody-mediated inhibition of ITGB5 (integrin αvβ5 in the KO line rescued the low expression of Nanog on Day 5, suggesting the regulation of Nanog transcription by Prnp via this Itgb5. mRNA expression analysis of the PRNP-related proteins PRND (Doppel and SPRN (Shadoo, whose PRNP function is known to be redundant, revealed their incapacity to compensate for the absence of PRNP during early ESC differentiation. Our findings provide strong evidence for a relationship between Prnp and several key pluripotency genes and attribute Prnp a crucial role in regulating self-renewal/differentiation status of ESC, confirming the participation of PRNP during early embryogenesis.

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

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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.

Population and genomic lessons from genetic analysis of two Indian populations.

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Juyal, Garima; Mondal, Mayukh; Luisi, Pierre; Laayouni, Hafid; Sood, Ajit; Midha, Vandana; Heutink, Peter; Bertranpetit, Jaume; Thelma, B K; Casals, Ferran

2014-10-01

Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

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C. MAGGI

2015-09-01

Full Text Available Parastichopus regalis (Cuvier, 1817 is the most expensive seafood product on the catalonian market (NE Spain, with prices around 130 €/Kg (fresh weight. Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia. We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST, AMOVA and correspondence analysis (CA based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1 an accurate assessment of the stocks status along the Spanish coasts; 2 the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3 the founding of protected areas (i.e. not take zones to conserve healthy populations and favour the recruitment on the nearby areas.

A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.

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Kasulin, Luciana; Rowan, Beth A; León, Rolando J C; Schuenemann, Verena J; Weigel, Detlef; Botto, Javier F

2017-07-01

The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500-km 2 -area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole-genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. admixture and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in the expression of phytochrome signalling genes. Pat had higher PIF3 and PIF5 and lower HY5 expression under Rc light; and lower expression of PIL1, ATHB2 and HFR1 under shade compared to Col-0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparison with other introduced populations will provide additional information for association studies and allow for a more detailed assessment of the demographic events following colonization. © 2017 John Wiley & Sons Ltd.

Effect of coumarins on HL-60 cell differentiation.

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Kawaii, S; Tomono, Y; Katase, E; Ogawa, K; Yano, M

2000-01-01

Twenty-eight coumarins, including 7 furocoumarins, were examined for their activity of induction of terminal differentiation of human promyelocytic leukemia cells (HL-60) by nitro blue tetrazolium (NBT) reducing, nonspecific esterase, specific esterase and phagocytic activities. Esculetin, nordalbergin, 6,7-dihydroxy-4-methylcoumarin and imperatorin had strong activity among the coumarins examined. HL-60 cells treated with these coumarins differentiated into mature monocyte/macrophage. The structure-activity relationship established from the results revealed that 6,7-dihydroxy moiety had an important role in the induction of differentiation of HL-60.

Hierarchical structure of ecological and non-ecological processes of differentiation shaped ongoing gastropod radiation in the Malawi Basin.

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Van Bocxlaer, Bert

2017-09-13

Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographical setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity. © 2017 The Author(s).

MAINTENANCE OF ECOLOGICALLY SIGNIFICANT GENETIC VARIATION IN THE TIGER SWALLOWTAIL BUTTERFLY THROUGH DIFFERENTIAL SELECTION AND GENE FLOW.

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Bossart, J L; Scriber, J M

1995-12-01

Differential selection in a heterogeneous environment is thought to promote the maintenance of ecologically significant genetic variation. Variation is maintained when selection is counterbalanced by the homogenizing effects of gene flow and random mating. In this study, we examine the relative importance of differential selection and gene flow in maintaining genetic variation in Papilio glaucus. Differential selection on traits contributing to successful use of host plants (oviposition preference and larval performance) was assessed by comparing the responses of southern Ohio, north central Georgia, and southern Florida populations of P. glaucus to three hosts: Liriodendron tulipifera, Magnolia virginiana, and Prunus serotina. Gene flow among populations was estimated using allozyme frequencies from nine polymorphic loci. Significant genetic differentiation was observed among populations for both oviposition preference and larval performance. This differentiation was interpreted to be the result of selection acting on Florida P. glaucus for enhanced use of Magnolia, the prevalent host in Florida. In contrast, no evidence of population differentiation was revealed by allozyme frequencies. F ST -values were very small and Nm, an estimate of the relative strengths of gene flow and genetic drift, was large, indicating that genetic exchange among P. glaucus populations is relatively unrestricted. The contrasting patterns of spatial differentiation for host-use traits and lack of differentiation for electrophoretically detectable variation implies that differential selection among populations will be counterbalanced by gene flow, thereby maintaining genetic variation for host-use traits. © 1995 The Society for the Study of Evolution.

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.

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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

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

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...... and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability...

Pdx1 and Ngn3 overexpression enhances pancreatic differentiation of mouse ES cell-derived endoderm population.

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Kubo, Atsushi; Stull, Robert; Takeuchi, Mitsuaki; Bonham, Kristina; Gouon-Evans, Valerie; Sho, Masayuki; Iwano, Masayuki; Saito, Yoshihiko; Keller, Gordon; Snodgrass, Ralph

2011-01-01

In order to define the molecular mechanisms regulating the specification and differentiation of pancreatic β-islet cells, we investigated the effect of upregulating Pdx1 and Ngn3 during the differentiation of the β-islet-like cells from murine embryonic stem (ES) cell-derived activin induced-endoderm. Induced overexpression of Pdx1 resulted in a significant upregulation of insulin (Ins1 and Ins2), and other pancreas-related genes. To enhance the developmental progression from the pancreatic bud to the formation of the endocrine lineages, we induced the overexpression express of Ngn3 together with Pdx1. This combination dramatically increased the level and timing of maximal Ins1 mRNA expression to approximately 100% of that found in the βTC6 insulinoma cell line. Insulin protein and C-peptide expression was confirmed by immunohistochemistry staining. These inductive effects were restricted to c-kit(+) endoderm enriched EB-derived populations suggesting that Pdx1/Ngn3 functions after the specification of pancreatic endoderm. Although insulin secretion was stimulated by various insulin secretagogues, these cells had only limited glucose response. Microarray analysis was used to evaluate the expression of a broad spectrum of pancreatic endocrine cell-related genes as well as genes associated with glucose responses. Taken together, these findings demonstrate the utility of manipulating Pdx1 and Ngn3 expression in a stage-specific manner as an important new strategy for the efficient generation of functionally immature insulin-producing β-islet cells from ES cells.

Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups

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Rajkumar, Revathi; Kashyap, VK

2004-01-01

Background A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. Results Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. Conclusion The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern

Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups

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Rajkumar Revathi

2004-08-01

Full Text Available Abstract Background A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. Results Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. Conclusion The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was

Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups.

Science.gov (United States)

Rajkumar, Revathi; Kashyap, V K

2004-08-19

A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them

Genetic population structure of the vulnerable bog fritillary butterfly.

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Vandewoestijne, S; Baguette, M

2004-01-01

Populations of the bog fritillary butterfly Proclossiana eunomia (Lepidoptera, Nymphalidae) occur in patchy habitat in central and western Europe. P. eunomia is a vulnerable species in the Belgian Ardennes and the number of occupied sites has significantly decreased in this region since the 1960s. RAPD (random amplified polymorphic DNA) markers were used to study the consequences of habitat loss and fragmentation on the genetic population structure of this species. Gene diversity was lower in populations with smaller population sizes. Genetic subdivision was high (Fst=0.0887) considering the small spatial scale of this study (150 km2). The most geographically isolated population was also the most genetically differentiated one. The genetic population structure and genetic differentiation detected in this study were explained by (1) differences in altitude of the sampled locations and, (2) lower dispersal propensity and dispersal rate in fragmented landscapes versus continuous landscapes. Results from the RAPD analyses were compared with a previous allozyme based study on the same populations. The results of this study suggest that increased fragmentation has lead to a greater genetic differentiation between remaining P. eunomia populations.

Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan

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Nishiyama, Takeshi; Kishino, Hirohisa; Suzuki, Sadao; Ando, Ryosuke; Niimura, Hideshi; Uemura, Hirokazu; Horita, Mikako; Ohnaka, Keizo; Kuriyama, Nagato; Mikami, Haruo; Takashima, Naoyuki; Mastuo, Keitaro; Guang, Yin; Wakai, Kenji; Hamajima, Nobuyuki; Tanaka, Hideo

2012-01-01

Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating FST among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study. PMID:22509376

Typing of 111 ancestry informative markers in an Albanian population

DEFF Research Database (Denmark)

Ribeiro, Joana; Pereira, V.; Kondili, A.

2015-01-01

) with the purpose of differentiating Middle Eastern populations from those of the rest of the world (publication in preparation). Before these multiplexes can be applied in forensic case work, population data for these markers are needed.In this work, samples from 51 Albanian individuals were typed with the AIMs...... script in the software R.The results were compared to other population samples previously typed for the same markers. The panel of AIMs was capable of differentiating the Albanian population from other population groups except for the Greek population. These results were expected due to the history...

Non-instantaneous impulses in differential equations

CERN Document Server

Agarwal, Ravi; O'Regan, Donal

2017-01-01

This monograph is the first published book devoted to the theory of differential equations with non-instantaneous impulses. It aims to equip the reader with mathematical models and theory behind real life processes in physics, biology, population dynamics, ecology and pharmacokinetics. The authors examine a wide scope of differential equations with non-instantaneous impulses through three comprehensive chapters, providing an all-rounded and unique presentation on the topic, including: - Ordinary differential equations with non-instantaneous impulses (scalar and n-dimensional case) - Fractional differential equa tions with non-instantaneous impulses (with Caputo fractional derivatives of order q ϵ (0, 1)) - Ordinary differential equations with non-instantaneous impulses occurring at random moments (with exponential, Erlang, or Gamma distribution) Each chapter focuses on theory, proofs and examples, and contains numerous graphs to enrich the reader’s understanding. Additionally, a carefully selected bibliogr...

Spatial genetic structure and mitochondrial DNA phylogeography of Argentinean populations of the grasshopper Dichroplus elongatus.

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Natalia Rosetti

Full Text Available Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD and partial sequences of the cytochrome oxydase 1 (COI mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the

Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus across Africa

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Bezault Etienne

2011-12-01

Full Text Available Abstract Background Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian (RST = 0.38 - 0.69. This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (RST = 0.24 - 0.32. The lowest differentiations were observed among connected populations within a basin (RST = 0.015 in the Volta basin. Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053. The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m ~ 0.094 - 0.097 in the Volta populations. Conclusions This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were

Genetic population structure of the desert shrub species lycium ruthenicum inferred from chloroplast dna

International Nuclear Information System (INIS)

Chen, H.; Yonezawa, T.

2014-01-01

Lycium ruthenicum (Solananeae), a spiny shrub mostly distributed in the desert regions of north and northwest China, has been shown to exhibit high tolerance to the extreme environment. In this study, the phylogeography and evolutionary history of L. ruthenicum were examined, on the basis of 80 individuals from eight populations. Using the sequence variations of two spacer regions of chloroplast DNA (trnH-psbA and rps16-trnK) , the absence of a geographic component in the chloroplast DNA genetic structure was identified (GST = 0.351, NST = 0.304, NST< GST), which was consisted with the result of SAMOVA, suggesting weak phylogeographic structure of this species. Phylogenetic and network analyses showed that a total of 10 haplotypes identified in the present study clustered into two clades, in which clade I harbored the ancestral haplotypes that inferred two independent glacial refugia in the middle of Qaidam Basin and the western Inner Mongolia. The existence of regional evolutionary differences was supported by GENETREE, which revealed that one of the population in Qaidam Basin and the two populations in Tarim Basin had experienced rapid expansion, and the other populations retained relatively stable population size during the Pleistocene . Given the results of long-term gene flow and pairwise differences, strong gene flow was insufficient to reduce the genetic differentiation among populations or within populations, probably due to the genetic composition containing a common haplotype and the high number of private haplotypes fixed for most of the population. The divergence times of different lineages were consistent with the rapid uplift phases of the Qinghai-Tibetan Plateau and the initiation and expansion of deserts in northern China, suggesting that the origin and evolution of L. ruthenicum were strongly influenced by Quaternary environment changes. (author)

Microsatellite analysis in two populations of Kunming mice

DEFF Research Database (Denmark)

Shang, Haitao; Wei, Hong; Yue, Bingfei

2009-01-01

populations are unclear. Fifteen microsatellite markers were screened by a fluorescence-based semi-automated genotyping method for the two main populations of Kunming mice from Beijing (BJ) and Shanghai (SH) in China. The observed number of alleles, effective number of alleles, observed heterozygosity......Kunming mice are the most widely used outbred colony in China. Differences in biological characters and drug reactions among different populations have been observed when using Kunming mice. But the molecular genetic profiles of Kunming mice and the extent of genetic differentiation among...... that there is abundant genetic variation in the populations of Kunming mice. Population differentiation was shown by shared alleles, F-statistics, Nei genetic distance and Nei genetic identity. In population BJ and population SH, respectively, only 35 of 61 and 35 of 63 alleles were shared by both. The Fst per locus...

Evaluating construct validity of the second version of the Copenhagen Psychosocial Questionnaire through analysis of differential item functioning and differential item effect

DEFF Research Database (Denmark)

Bjorner, Jakob Bue; Pejtersen, Jan Hyld

2010-01-01

AIMS: To evaluate the construct validity of the Copenhagen Psychosocial Questionnaire II (COPSOQ II) by means of tests for differential item functioning (DIF) and differential item effect (DIE). METHODS: We used a Danish general population postal survey (n = 4,732 with 3,517 wage earners) with a ...

Rapid differentiation of Listeria monocytogenes epidemic clones III and IV and their intact compared with heat-killed populations using Fourier transform infrared spectroscopy and chemometrics.

Science.gov (United States)

Nyarko, Esmond B; Puzey, Kenneth A; Donnelly, Catherine W

2014-06-01

The objectives of this study were to determine if Fourier transform infrared (FT-IR) spectroscopy and multivariate statistical analysis (chemometrics) could be used to rapidly differentiate epidemic clones (ECs) of Listeria monocytogenes, as well as their intact compared with heat-killed populations. FT-IR spectra were collected from dried thin smears on infrared slides prepared from aliquots of 10 μL of each L. monocytogenes ECs (ECIII: J1-101 and R2-499; ECIV: J1-129 and J1-220), and also from intact and heat-killed cell populations of each EC strain using 250 scans at a resolution of 4 cm(-1) in the mid-infrared region in a reflectance mode. Chemometric analysis of spectra involved the application of the multivariate discriminant method for canonical variate analysis (CVA) and linear discriminant analysis (LDA). CVA of the spectra in the wavelength region 4000 to 600 cm(-1) separated the EC strains while LDA resulted in a 100% accurate classification of all spectra in the data set. Further, CVA separated intact and heat-killed cells of each EC strain and there was 100% accuracy in the classification of all spectra when LDA was applied. FT-IR spectral wavenumbers 1650 to 1390 cm(-1) were used to separate heat-killed and intact populations of L. monocytogenes. The FT-IR spectroscopy method allowed discrimination between strains that belong to the same EC. FT-IR is a highly discriminatory and reproducible method that can be used for the rapid subtyping of L. monocytogenes, as well as for the detection of live compared with dead populations of the organism. Fourier transform infrared (FT-IR) spectroscopy and multivariate statistical analysis can be used for L. monocytogenes source tracking and for clinical case isolate comparison during epidemiological investigations since the method is capable of differentiating epidemic clones and it uses a library of well-characterized strains. The FT-IR method is potentially less expensive and more rapid compared to genetic

Population genetic structure of Taenia solium from Madagascar and Mexico: implications for clinical profile diversity and immunological technology.

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Vega, Rodrigo; Piñero, Daniel; Ramanankandrasana, Bienvenue; Dumas, Michel; Bouteille, Bernard; Fleury, Agnes; Sciutto, Edda; Larralde, Carlos; Fragoso, Gladis

2003-11-01

Taenia solium is a cestode parasitic of humans and pigs that strongly impacts on public health in developing countries. Its larvae (cysticercus) lodge in the brain, causing neurocysticercosis, and in other tissues, like skeletal muscle and subcutaneous space, causing extraneuronal cysticercosis. Prevalences of these two clinical manifestations vary greatly among continents. Also, neurocysticercosis may be clinically heterogeneous, ranging from asymptomatic forms to severely incapacitating and even fatal presentation. Further, vaccine design and diagnosis technology have met with difficulties in sensitivity, specificity and reproducibility. Parasite diversity underlying clinical heterogeneity and technological difficulties is little explored. Here, T. solium genetic population structure and diversity was studied by way of random amplified polymorphic DNA in individual cysticerci collected from pigs in Madagascar and two regions in Mexico. The amplification profiles of T. solium were also compared with those of the murine cysticercus Taenia crassiceps (ORF strain). We show significant genetic differentiation between Madagascar and Mexico and between regions in Mexico, but less so between cysticerci from different localities in Mexico and none between cysticerci from different tissues from the same pig. We also found restricted genetic variability within populations and gene flow was estimated to be low between populations. Thus, genetic differentiation of T. solium suggests that different evolutionary paths have been taken and provides support for its involvement in the differential tissue distribution of cysticerci and varying degrees of severity of the disease. It may also explain difficulties in the development of vaccines and tools for immunodiagnosis.

Population genetic structure of urban malaria vector Anopheles stephensi in India.

Science.gov (United States)

Sharma, Richa; Sharma, Arvind; Kumar, Ashwani; Dube, Madhulika; Gakhar, S K

2016-04-01

Malaria is a major public health problem in India because climatic condition and geography of India provide an ideal environment for development of malaria vector. Anopheles stephensi is a major urban malaria vector in India and its control has been hampered by insecticide resistance. In present study population genetic structure of A. stephensi is analyzed at macro geographic level using 13 microsatellite markers. Significantly high genetic differentiation was found in all studied populations with differentiation values (FST) ranging from 0.0398 to 0.1808. The geographic distance was found to be playing a major role in genetic differentiation between different populations. Overall three genetic pools were observed and population of central India was found to be coexisting in two genetic pools. High effective population size (Ne) was found in all the studied populations. Copyright © 2015 Elsevier B.V. All rights reserved.

Stem cell-like differentiation potentials of endometrial side population cells as revealed by a newly developed in vivo endometrial stem cell assay.

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Kaoru Miyazaki

Full Text Available Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP, but not endometrial main population cells (EMP, exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay.ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom, a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells.We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo endometrial tissue reconstitution. Using this assay, we demonstrated that ESP

The roles of geography and founder effects in promoting host-associated differentiation in the generalist bogus yucca moth Prodoxus decipiens.

Science.gov (United States)

Darwell, C T; Fox, K A; Althoff, D M

2014-12-01

There is ample evidence that host shifts in plant-feeding insects have been instrumental in generating the enormous diversity of insects. Changes in host use can cause host-associated differentiation (HAD) among populations that may lead to reproductive isolation and eventual speciation. The importance of geography in facilitating this process remains controversial. We examined the geographic context of HAD in the wide-ranging generalist yucca moth Prodoxus decipiens. Previous work demonstrated HAD among sympatric moth populations feeding on two different Yucca species occurring on the barrier islands of North Carolina, USA. We assessed the genetic structure of P. decipiens across its entire geographic and host range to determine whether HAD is widespread in this generalist herbivore. Population genetic analyses of microsatellite and mtDNA sequence data across the entire range showed genetic structuring with respect to host use and geography. In particular, genetic differentiation was relatively strong between mainland populations and those on the barrier islands of North Carolina. Finer scale analyses, however, among sympatric populations using different host plant species only showed significant clustering based on host use for populations on the barrier islands. Mainland populations did not form population clusters based on host plant use. Reduced genetic diversity in the barrier island populations, especially on the derived host, suggests that founder effects may have been instrumental in facilitating HAD. In general, results suggest that the interplay of local adaptation, geography and demography can determine the tempo of HAD. We argue that future studies should include comprehensive surveys across a wide range of environmental and geographic conditions to elucidate the contribution of various processes to HAD. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

Science.gov (United States)

Duc, N M; Duy, V D; Xuan, B T T; Thang, B V; Ha, N T H; Tam, N M

2016-10-24

Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (N A = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise F ST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising

A Qualitative Analysis of the Neutron Population in Fresh and Spent Fuel Assemblies during Simulated Interrogation using the Differential Die-Away Technique

International Nuclear Information System (INIS)

Lundkvista, Niklas; Goodsell, Alison V.; Grapea, Sophie; Hendricksb, John S.; Henzlb, Vladimir; Swinhoe, Martyn T.; Tobin, Stephen J.

2015-01-01

Monte Carlo simulations were performed for the differential die-away (DDA) technique to analyse the time-dependent behaviour of the neutron population in fresh and spent nuclear fuel assemblies as part of the Next Generation Safeguards Initiative Spent Fuel (NGSI-SF) Project. Simulations were performed to investigate both a possibly portable as well as a permanent DDA instrument. Taking advantage of a custom made modification to the MCNPX code, the variation in the neutron population, simultaneously in time and space, was examined. The motivation for this research was to improve the design of the DDA instrument, as it is being considered for possible deployment at the Central Storage of Spent Nuclear Fuel and Encapsulation Plant in Sweden (Clab), as well as to assist in the interpretation of the both simulated and measured signals.

Modelling effects of diquat under realistic exposure patterns in genetically differentiated populations of the gastropod Lymnaea stagnalis.

Science.gov (United States)

Ducrot, Virginie; Péry, Alexandre R R; Lagadic, Laurent

2010-11-12

Pesticide use leads to complex exposure and response patterns in non-target aquatic species, so that the analysis of data from standard toxicity tests may result in unrealistic risk forecasts. Developing models that are able to capture such complexity from toxicity test data is thus a crucial issue for pesticide risk assessment. In this study, freshwater snails from two genetically differentiated populations of Lymnaea stagnalis were exposed to repeated acute applications of environmentally realistic concentrations of the herbicide diquat, from the embryo to the adult stage. Hatching rate, embryonic development duration, juvenile mortality, feeding rate and age at first spawning were investigated during both exposure and recovery periods. Effects of diquat on mortality were analysed using a threshold hazard model accounting for time-varying herbicide concentrations. All endpoints were significantly impaired at diquat environmental concentrations in both populations. Snail evolutionary history had no significant impact on their sensitivity and responsiveness to diquat, whereas food acted as a modulating factor of toxicant-induced mortality. The time course of effects was adequately described by the model, which thus appears suitable to analyse long-term effects of complex exposure patterns based upon full life cycle experiment data. Obtained model outputs (e.g. no-effect concentrations) could be directly used for chemical risk assessment.

Lack of genetic differentiation between contrasted overwintering strategies of a major pest predator Episyrphus balteatus (Diptera: Syrphidae: implications for biocontrol.

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Lucie Raymond

Full Text Available Winter ecology of natural enemies has a great influence on the level and efficiency of biological control at spring. The hoverfly Episyrphus balteatus (DeGeer (Diptera: Syrphidae is one of the most important natural predators of crop aphids in Europe. Three different overwintering strategies coexist in this species which makes it a good model in order to study ecologically-based speciation processes. The purpose of this study was to determine whether E. balteatus populations with alternative overwintering strategies are genetically differentiated. To that aim, we developed 12 specific microsatellite markers and evaluated the level of neutral genetic differentiation between E. balteatus field populations that overwinter in the three different ways described in this species (i.e. migration, local overwintering at a pre-imaginal stage, and local overwintering at adult stage. Results showed a lack of neutral genetic differentiation between individuals with different overwintering strategies although there are strong ecological differences between them. All pair-wise FST values are below 0.025 and non-significant, and Bayesian clustering showed K=1 was the most likely number of genetic clusters throughout our sample. The three overwintering strategies form one unique panmictic population. This suggests that all the individuals may have genetic material for the expression of different overwintering phenotypes, and that their commitment in one particular overwintering strategy may depend on environmental and individual factors. Consequently, the prevalence of the different overwintering strategies would be potentially modified by landscape engineering and habitat management which could have major implications for biological control.

Traveltime dispersion in an isotropic elastic mantle: strong lower-mantle signal in differential-frequency residuals

Science.gov (United States)

Schuberth, Bernhard S. A.; Zaroli, Christophe; Nolet, Guust

2015-12-01

We study wavefield effects of direct P- and S-waves in elastic and isotropic 3-D seismic structures derived from the temperature field of a high-resolution mantle circulation model. More specifically, we quantify the dispersion of traveltime residuals caused by diffraction in structures with dynamically constrained length scales and magnitudes of the lateral variations in seismic velocities and density. 3-D global wave propagation is simulated using a spectral element method. Intrinsic attenuation (i.e. dissipation of seismic energy) is deliberately neglected, so that any variation of traveltimes with frequency can be attributed to structural effects. Traveltime residuals are measured at 15, 22.5, 34 and 51 s dominant periods by cross-correlation of 3-D and 1-D synthetic waveforms. Additional simulations are performed for a model in which 3-D structure is removed in the upper 800 km to isolate the dispersion signal of the lower mantle. We find that the structural length scales inherent to a vigorously convecting mantle give rise to significant diffraction-induced body-wave traveltime dispersion. For both P- and S-waves, the difference between long-period and short-period residuals for a given source-receiver pair can reach up to several seconds for the period bands considered here. In general, these `differential-frequency' residuals tend to increase in magnitude with increasing short-period delay. Furthermore, the long-period signal typically is smaller in magnitude than the short-period one; that is, wave-front healing is efficient independent of the sign of the residuals. Unlike the single-frequency residuals, the differential-frequency residuals are surprisingly similar between the `lower-mantle' and the `whole-mantle' model for corresponding source-receiver pairs. The similarity is more pronounced in case of S-waves and varies between different combinations of period bands. The traveltime delay acquired in the upper mantle seems to cancel in these differential

Ascaroside expression in Caenorhabditis elegans is strongly dependent on diet and developmental stage.

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Fatma Kaplan

2011-03-01

Full Text Available The ascarosides form a family of small molecules that have been isolated from cultures of the nematode Caenorhabditis elegans. They are often referred to as "dauer pheromones" because most of them induce formation of long-lived and highly stress resistant dauer larvae. More recent studies have shown that ascarosides serve additional functions as social signals and mating pheromones. Thus, ascarosides have multiple functions. Until now, it has been generally assumed that ascarosides are constitutively expressed during nematode development.Cultures of C. elegans were developmentally synchronized on controlled diets. Ascarosides released into the media, as well as stored internally, were quantified by LC/MS. We found that ascaroside biosynthesis and release were strongly dependent on developmental stage and diet. The male attracting pheromone was verified to be a blend of at least four ascarosides, and peak production of the two most potent mating pheromone components, ascr#3 and asc#8 immediately preceded or coincided with the temporal window for mating. The concentration of ascr#2 increased under starvation conditions and peaked during dauer formation, strongly supporting ascr#2 as the main population density signal (dauer pheromone. After dauer formation, ascaroside production largely ceased and dauer larvae did not release any ascarosides. These findings show that both total ascaroside production and the relative proportions of individual ascarosides strongly correlate with these compounds' stage-specific biological functions.Ascaroside expression changes with development and environmental conditions. This is consistent with multiple functions of these signaling molecules. Knowledge of such differential regulation will make it possible to associate ascaroside production to gene expression profiles (transcript, protein or enzyme activity and help to determine genetic pathways that control ascaroside biosynthesis. In conjunction with findings

Comparative population structure of cavity-nesting sea ducks

Science.gov (United States)

Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

2014-01-01

A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

Analysis of an age structured model for tick populations subject to seasonal effects

Science.gov (United States)

Liu, Kaihui; Lou, Yijun; Wu, Jianhong

2017-08-01

We investigate an age-structured hyperbolic equation model by allowing the birth and death functions to be density dependent and periodic in time with the consideration of seasonal effects. By studying the integral form solution of this general hyperbolic equation obtained through the method of integration along characteristics, we give a detailed proof of the uniqueness and existence of the solution in light of the contraction mapping theorem. With additional biologically natural assumptions, using the tick population growth as a motivating example, we derive an age-structured model with time-dependent periodic maturation delays, which is quite different from the existing population models with time-independent maturation delays. For this periodic differential system with seasonal delays, the basic reproduction number R0 is defined as the spectral radius of the next generation operator. Then, we show the tick population tends to die out when R0 1. When there is no intra-specific competition among immature individuals due to the sufficient availability of immature tick hosts, the global stability of the positive periodic state for the whole model system of four delay differential equations can be obtained with the observation that a scalar subsystem for the adult stage size can be decoupled. The challenge for the proof of such a global stability result can be overcome by introducing a new phase space, based on which, a periodic solution semiflow can be defined which is eventually strongly monotone and strictly subhomogeneous.

Pdx1 and Ngn3 overexpression enhances pancreatic differentiation of mouse ES cell-derived endoderm population.

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Atsushi Kubo

Full Text Available In order to define the molecular mechanisms regulating the specification and differentiation of pancreatic β-islet cells, we investigated the effect of upregulating Pdx1 and Ngn3 during the differentiation of the β-islet-like cells from murine embryonic stem (ES cell-derived activin induced-endoderm. Induced overexpression of Pdx1 resulted in a significant upregulation of insulin (Ins1 and Ins2, and other pancreas-related genes. To enhance the developmental progression from the pancreatic bud to the formation of the endocrine lineages, we induced the overexpression express of Ngn3 together with Pdx1. This combination dramatically increased the level and timing of maximal Ins1 mRNA expression to approximately 100% of that found in the βTC6 insulinoma cell line. Insulin protein and C-peptide expression was confirmed by immunohistochemistry staining. These inductive effects were restricted to c-kit(+ endoderm enriched EB-derived populations suggesting that Pdx1/Ngn3 functions after the specification of pancreatic endoderm. Although insulin secretion was stimulated by various insulin secretagogues, these cells had only limited glucose response. Microarray analysis was used to evaluate the expression of a broad spectrum of pancreatic endocrine cell-related genes as well as genes associated with glucose responses. Taken together, these findings demonstrate the utility of manipulating Pdx1 and Ngn3 expression in a stage-specific manner as an important new strategy for the efficient generation of functionally immature insulin-producing β-islet cells from ES cells.

Pricing strategies and service differentiation

NARCIS (Netherlands)

Mandjes, M.R.H.

2004-01-01

This paper analyzes a communication network, used by customers with heterogeneous service requirements. We investigate priority queueing as a way to establish service differentiation. It is assumed that there is an infinite population of customers, who join the network as long as their utility

Low genetic diversity and high genetic differentiation among ...

African Journals Online (AJOL)

Of a total of 26 known populations, 14 are now extinct, five during the course of this study. Action to prevent complete extinction of the species is therefore urgent. Keywords: Caesalpinioideae, Fabaceae, Ghana, inbreeding, population differentiation, RAPD, species extinction. Southern Forests 2011, 73(2): 73–80 ...

Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model.

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Anne Chao

Full Text Available Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1 unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2 these measures connect directly to the rich predictive mathematics of information theory; (3 Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4 Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation" between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model.

Science.gov (United States)

Chao, Anne; Jost, Lou; Hsieh, T C; Ma, K H; Sherwin, William B; Rollins, Lee Ann

2015-01-01

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Host phenology and geography as drivers of differentiation in generalist fungal mycoparasites.

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Alexandra Pintye

Full Text Available The question as to why parasites remain generalist or become specialist is a key unresolved question in evolutionary biology. Ampelomyces spp., intracellular mycoparasites of powdery mildew fungi, which are themselves plant pathogens, are a useful model for studies of this issue. Ampelomyces is used for the biological control of mildew. Differences in mycohost phenology promote temporal isolation between sympatric Ampelomyces mycoparasites. Apple powdery mildew (APM causes spring epidemics, whereas other powdery mildew species on plants other than apple cause epidemics later in the season. This has resulted in genetic differentiation between APM and non-APM strains. It is unclear whether there is genetic differentiation between non-APM Ampelomyces lineages due to their specialization on different mycohosts. We used microsatellites to address this question and found no significant differentiation between non-APM Ampelomyces strains from different mycohosts or host plants, but strong differentiation between APM and non-APM strains. A geographical structure was revealed in both groups, with differences between European countries, demonstrating restricted dispersal at the continent scale and a high resolution for our markers. We found footprints of recombination in both groups, possibly more frequent in the APM cluster. Overall, Ampelomyces thus appears to be one of the rare genuine generalist pathogenic fungi able to parasitize multiple hosts in natural populations. It is therefore an excellent model for studying the evolution of pathogens towards a generalist rather than host-specific strategy, particularly in light of the tritrophic interaction between Ampelomyces mycoparasites, their powdery mildew fungal hosts and the mildew host plants.

Socio-economic differentials in child stunting are consistently larger in urban than rural areas

OpenAIRE

Menon, Purnima; Ruel, Marie T.; Morris, Saul Sutkover

2000-01-01

Urban-rural comparisons of childhood undernutrition suggest that urban populations are better-off than rural populations. However, these comparisons could mask the large differentials that exist among socioeconomic groups in urban areas. Data from the Demographic and Health Surveys (DHS) for 11 countries from three regions were used to test the hypothesis that intra-urban differentials in child stunting were greater than intra-rural differentials, and that the prevalence of stunting among the...

The effect of temperature on Anopheles mosquito population dynamics and the potential for malaria transmission.

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Lindsay M Beck-Johnson

Full Text Available The parasites that cause malaria depend on Anopheles mosquitoes for transmission; because of this, mosquito population dynamics are a key determinant of malaria risk. Development and survival rates of both the Anopheles mosquitoes and the Plasmodium parasites that cause malaria depend on temperature, making this a potential driver of mosquito population dynamics and malaria transmission. We developed a temperature-dependent, stage-structured delayed differential equation model to better understand how climate determines risk. Including the full mosquito life cycle in the model reveals that the mosquito population abundance is more sensitive to temperature than previously thought because it is strongly influenced by the dynamics of the juvenile mosquito stages whose vital rates are also temperature-dependent. Additionally, the model predicts a peak in abundance of mosquitoes old enough to vector malaria at more accurate temperatures than previous models. Our results point to the importance of incorporating detailed vector biology into models for predicting the risk for vector borne diseases.

Plasmodium vivax populations revisited: mitochondrial genomes of temperate strains in Asia suggest ancient population expansion

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Miao Miao

2012-02-01

Full Text Available Abstract Background Plasmodium vivax is the most widely distributed human malaria parasite outside of Africa, and its range extends well into the temperate zones. Previous studies provided evidence for vivax population differentiation, but temperate vivax parasites were not well represented in these analyses. Here we address this deficit by using complete mitochondrial (mt genome sequences to elucidate the broad genetic diversity and population structure of P. vivax from temperate regions in East and Southeast Asia. Results From the complete mtDNA sequences of 99 clinical samples collected in China, Myanmar and Korea, a total of 30 different haplotypes were identified from 26 polymorphic sites. Significant differentiation between different East and Southeast Asian parasite populations was observed except for the comparison between populations from Korea and southern China. Haplotype patterns and structure diversity analysis showed coexistence of two different groups in East Asia, which were genetically related to the Southeast Asian population and Myanmar population, respectively. The demographic history of P. vivax, examined using neutrality tests and mismatch distribution analyses, revealed population expansion events across the entire P. vivax range and the Myanmar population. Bayesian skyline analysis further supported the occurrence of ancient P. vivax population expansion. Conclusions This study provided further resolution of the population structure and evolution of P. vivax, especially in temperate/warm-temperate endemic areas of Asia. The results revealed divergence of the P. vivax populations in temperate regions of China and Korea from other populations. Multiple analyses confirmed ancient population expansion of this parasite. The extensive genetic diversity of the P. vivax populations is consistent with phenotypic plasticity of the parasites, which has implications for malaria control.

Bodrum Strong Motion Network, Mugla, Turkey

Science.gov (United States)

Alcik, H. A.; Tanircan, G.; Korkmaz, A.

2015-12-01

The Gulf of Gökova is located in southwestern Turkey near the Aegean Sea and surrounded by Datça Peninsula to the south, the island of Kos to the west and Bodrum Peninsula to the north. The Bodrum peninsula with a population of one million in summer season is one of the most populated touristic centers of Turkey. This region is also surrounded by numerous active seismic entities such as Ula-Ören Fault Zone, Gökova Graben etc.. and demonstrates high seismic hazard. In the past, many destructive earthquakes have occurred in southwestern Turkey. One of the destructive historical earthquakes is 1493 Kos event (Mw=6.9) caused heavy damage in Bodrum. In the instrumental period seismic activity in the Gökova region includes the Ms>6.0 earthquakes of 23 April 1933 (Ms=6.4), 23 May 1941 (Ms=6.0), 13 December 1941 (Ms=6.5) events. Intense earthquake activity (Mw5+) occurred in Gulf of Gökova in August 2004 and January 2005. Considering the high seismicity and population of this region, a strong ground motion monitoring system stationed in dense settlements in the Bodrum Peninsula: Bodrum, Turgutreis, Yalıkavak, Çiftlik and Ortakent was deployed on June 2015. The network consists of 5 strong motion recorders, has been set up with the aim of monitoring of regional earthquakes, collecting accurate and reliable data for engineering and scientific research purposes, in particular to provide input for future earthquake rapid reporting and early warning implementation projects on urban environments in the Bodrum peninsula and the surrounding areas. In this poster presentation, we briefly introduce the Bodrum Network and discuss our future plans for further developments.

Differential effects of cocaine on histone posttranslational modifications in identified populations of striatal neurons.

Science.gov (United States)

Jordi, Emmanuelle; Heiman, Myriam; Marion-Poll, Lucile; Guermonprez, Pierre; Cheng, Shuk Kei; Nairn, Angus C; Greengard, Paul; Girault, Jean-Antoine

2013-06-04

Drugs of abuse, such as cocaine, induce changes in gene expression and epigenetic marks including alterations in histone posttranslational modifications in striatal neurons. These changes are thought to participate in physiological memory mechanisms and to be critical for long-term behavioral alterations. However, the striatum is composed of multiple cell types, including two distinct populations of medium-sized spiny neurons, and little is known concerning the cell-type specificity of epigenetic modifications. To address this question we used bacterial artificial chromosome transgenic mice, which express EGFP fused to the N-terminus of the large subunit ribosomal protein L10a driven by the D1 or D2 dopamine receptor (D1R, D2R) promoter, respectively. Fluorescence in nucleoli was used to sort nuclei from D1R- or D2R-expressing neurons and to quantify by flow cytometry the cocaine-induced changes in histone acetylation and methylation specifically in these two types of nuclei. The two populations of medium-sized spiny neurons displayed different patterns of histone modifications 15 min or 24 h after a single injection of cocaine or 24 h after seven daily injections. In particular, acetylation of histone 3 on Lys 14 and of histone 4 on Lys 5 and 12, and methylation of histone 3 on Lys 9 exhibited distinct and persistent changes in the two cell types. Our data provide insights into the differential epigenetic responses to cocaine in D1R- and D2R-positive neurons and their potential regulation, which may participate in the persistent effects of cocaine in these neurons. The method described should have general utility for studying nuclear modifications in different types of neuronal or nonneuronal cell types.

Divergence in morphology, but not habitat use, despite low genetic differentiation among insular populations of the lizard Anolis lemurinus in Honduras

Science.gov (United States)

Logan, M.L.; Montgomery, Chad E.; Boback, Scott M.; Reed, R.N.; Campbell, J.A.

2012-01-01

Studies of recently isolated populations are useful because observed differences can often be attributed to current environmental variation. Two populations of the lizard Anolis lemurinus have been isolated on the islands of Cayo Menor and Cayo Mayor in the Cayos Cochinos Archipelago of Honduras for less than 15 000 y. We measured 12 morphometric and 10 habitat-use variables on 220 lizards across these islands in 2 y, 2008 and 2009. The goals of our study were (1) to explore patterns of sexual dimorphism, and (2) to test the hypothesis that differences in environment among islands may have driven divergence in morphology and habitat use despite genetic homogeneity among populations. Although we found no differences among sexes in habitat use, males had narrower pelvic girdles and longer toe pads on both islands. Between islands, males differed in morphology, but neither males nor females differed in habitat use. Our data suggest that either recent selection has operated differentially on males despite low genetic dill'erentiation, or that they display phenotypic plasticity in response to environmental variation. We suggest that patterns may be driven by variation in intrapopulation density or differences in predator diversity among islands.

Algorithms For Integrating Nonlinear Differential Equations

Science.gov (United States)

Freed, A. D.; Walker, K. P.

1994-01-01

Improved algorithms developed for use in numerical integration of systems of nonhomogenous, nonlinear, first-order, ordinary differential equations. In comparison with integration algorithms, these algorithms offer greater stability and accuracy. Several asymptotically correct, thereby enabling retention of stability and accuracy when large increments of independent variable used. Accuracies attainable demonstrated by applying them to systems of nonlinear, first-order, differential equations that arise in study of viscoplastic behavior, spread of acquired immune-deficiency syndrome (AIDS) virus and predator/prey populations.

Differential Rotation via Tracking of Coronal Bright Points.

Science.gov (United States)

McAteer, James; Boucheron, Laura E.; Osorno, Marcy

2016-05-01

The accurate computation of solar differential rotation is important both as a constraint for, and evidence towards, support of models of the solar dynamo. As such, the use of Xray and Extreme Ultraviolet bright points to elucidate differential rotation has been studied in recent years. In this work, we propose the automated detection and tracking of coronal bright points (CBPs) in a large set of SDO data for re-evaluation of solar differential rotation and comparison to other results. The big data aspects, and high cadence, of SDO data mitigate a few issues common to detection and tracking of objects in image sequences and allow us to focus on the use of CBPs to determine differential rotation. The high cadence of the data allows to disambiguate individual CBPs between subsequent images by allowing for significant spatial overlap, i.e., by the fact that the CBPs will rotate a short distance relative to their size. The significant spatial overlap minimizes the effects of incorrectly detected CBPs by reducing the occurrence of outlier values of differential rotation. The big data aspects of the data allows to be more conservative in our detection of CBPs (i.e., to err on the side of missing CBPs rather than detecting extraneous CBPs) while still maintaining statistically larger populations over which to study characteristics. The ability to compute solar differential rotation through the automated detection and tracking of a large population of CBPs will allow for further analyses such as the N-S asymmetry of differential rotation, variation of differential rotation over the solar cycle, and a detailed study of the magnetic flux underlying the CBPs.

COLONIZATION AND DIFFERENTIATION IN THE CLONAL PERENNIAL AGROSTIS-STOLONIFERA

NARCIS (Netherlands)

Kik, C; van Andel, Jelte; van Delden, Wilke; Joenje, W; Bijlsma, Rudolf

1990-01-01

(1) Colonization and differentiation were studied in four populations (inland meadow, salt-marsh, polder and sand-dune) of the widespread grass Agrostis stolonifera. A common-garden experiment showed that the overall population variability could be divided, through the use of principal component

Genetic diversity in wild populations of Paulownia fortune.

Science.gov (United States)

Li, H Y; Ru, G X; Zhang, J; Lu, Y Y

2014-11-01

The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138-1.2726), Nei's genetic diversity (0.1566-0.1887), and Shannon's information index (0.2692-0.3117) indicated a plentiful genetic diversity and different among Paulownia fortunei populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.

Epigenetic landscapes reveal transcription factors regulating CD8+ T cell differentiation

Science.gov (United States)

Yu, Bingfei; Zhang, Kai; Milner, J. Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P.; Pereira, Renata M.; Crotty, Shane; Chang, John T.; Pipkin, Matthew E.; Wang, Wei; Goldrath, Ananda W.

2017-01-01

Dynamic changes in the expression of transcription factors (TFs) can influence specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TF among differentially-fated precursor cells suggests additional underlying mechanisms. Here, we profiled genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that TF expression and binding contributed to establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal novel TFs influencing the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector and memory-precursor cell-fates, respectively. Our data define the epigenetic landscape of differentiation intermediates, facilitating identification of TFs with previously unappreciated roles in CD8+ T cell differentiation. PMID:28288100

Making a stand: five centuries of population growth in colonizing populations of Pinus ponderosa.

Science.gov (United States)

Lesser, Mark R; Jackson, Stephen T

2012-05-01

The processes underlying the development of new populations are important for understanding how species colonize new territory and form viable long-term populations. Life-history-mediated processes such as Allee effects and dispersal capability may interact with climate variability and site-specific factors to govern population success and failure over extended time frames. We studied four disjunct populations of ponderosa pine in the Bighorn Basin of north-central Wyoming to examine population growth spanning more than five centuries. The study populations are separated from continuous ponderosa pine forest by distances ranging from 15 to >100 km. Strong evidence indicates that the initial colonizing individuals are still present, yielding a nearly complete record of population history. All trees in each population were aged using dendroecological techniques. The populations were all founded between 1530 and 1655 cal yr CE. All show logistic growth patterns, with initial exponential growth followed by a slowing during the mid to late 20th century. Initial population growth was slower than expectations from a logistic regression model at all four populations, but increased during the mid-18th century. Initial lags in population growth may have been due to strong Allee effects. A combination of overcoming Allee effects and a transition to favorable climate conditions may have facilitated a mid-18th century pulse in population growth rate.

DYNAMICS OF Cercospora zeina POPULATIONS IN MAIZE-BASED ...

African Journals Online (AJOL)

ACSS

DYNAMICS OFCercospora zeina POPULATIONS IN MAIZE-BASED AGRO- ..... Population differentiation of Cercospora zeina in three districts of Uganda based on analysis of molecular variance ..... interactions: The example of the Erysiphe.

Type 2 diabetes mellitus susceptibility gene TCF7L2 is strongly associated with hyperglycemia in the Saudi Arabia Population of the eastern province of Saudi Arabia.

Science.gov (United States)

Acharya, S; Al-Elq, A; Al-Nafaie, A; Muzaheed, M; Al-Ali, A

2015-08-01

We studied the association of single nucleotide polymorphisms (SNPs) rs7903146, rs12255372 and rs4506565 in type 2 diabetes mellitus (T2DM) susceptibility gene, transcription factor 7 like 2 (TCF7L2) with T2DM among the population of the Eastern Province of Saudi Arabia. In a case-control study, blood samples were collected from 359 T2DM patients and 351 age and sex-matched normoglycemic controls. Genotyping was done by allele specific PCR assay. Our results revealed a strong association between risk T alleles in variants rs12255372 (OR: G/T=1.4233; T/T=2.0395) and rs4506565 (OR: A/T=1.6066; T/T=3.1301) and T2DM among the Saudi population of the Eastern Province of Saudi Arabia. This is the first time that this association has been identified in a Saudi population. However, a common variant, rs7903146, often found to be associated with T2DM in other populations failed to demonstrate any association to T2DM with the present population. These data further strengthens the hypothesis that Saudi populations might carry a distinct risk allele in T2DM susceptibility gene TCF7L2. The present results confirm that rs12255372 and rs4506565 variants of TCF7L2 show an association, but not rs7903146, with T2DM for the Saudi population of the Eastern Province of Saudi Arabia.

An Alu-like RNA promotes cell differentiation and reduces malignancy of human neuroblastoma cells.

Science.gov (United States)

Castelnuovo, Manuele; Massone, Sara; Tasso, Roberta; Fiorino, Gloria; Gatti, Monica; Robello, Mauro; Gatta, Elena; Berger, Audrey; Strub, Katharina; Florio, Tullio; Dieci, Giorgio; Cancedda, Ranieri; Pagano, Aldo

2010-10-01

Neuroblastoma (NB) is a pediatric cancer characterized by remarkable cell heterogeneity within the tumor nodules. Here, we demonstrate that the synthesis of a pol III-transcribed noncoding (nc) RNA (NDM29) strongly restricts NB development by promoting cell differentiation, a drop of malignancy processes, and a dramatic reduction of the tumor initiating cell (TIC) fraction in the NB cell population. Notably, the overexpression of NDM29 also confers to malignant NB cells an unpredicted susceptibility to the effects of antiblastic drugs used in NB therapy. Altogether, these results suggest the induction of NDM29 expression as possible treatment to increase cancer cells vulnerability to therapeutics and the measure of its synthesis in NB explants as prognostic factor of this cancer type.

Existence and stability of periodic solutions of an impulsive differential equation and application to CD8 T-cell differentiation.

Science.gov (United States)

Girel, Simon; Crauste, Fabien

2018-06-01

Unequal partitioning of the molecular content at cell division has been shown to be a source of heterogeneity in a cell population. We propose to model this phenomenon with the help of a scalar, nonlinear impulsive differential equation (IDE). To study the effect of molecular partitioning at cell division on the effector/memory cell-fate decision in a CD8 T-cell lineage, we study an IDE describing the concentration of the protein Tbet in a CD8 T-cell, where impulses are associated to cell division. We discuss how the degree of asymmetry of molecular partitioning can affect the process of cell differentiation and the phenotypical heterogeneity of a cell population. We show that a moderate degree of asymmetry is necessary and sufficient to observe irreversible differentiation. We consider, in a second part, a general autonomous IDE with fixed times of impulse and a specific form of impulse function. We establish properties of the solutions of that equation, most of them obtained under the hypothesis that impulses occur periodically. In particular, we show how to investigate the existence of periodic solutions and their stability by studying the flow of an autonomous differential equation. Then we apply those properties to prove the results presented in the first part.

Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

Science.gov (United States)

Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

2005-08-01

ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow

Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands.

Science.gov (United States)

Sun, Ye; Vargas-Mendoza, Carlos F

2017-01-01

Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

Directory of Open Access Journals (Sweden)

Ye Sun

2017-06-01

Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

Population genetic structure of rare and endangered plants using molecular markers

Science.gov (United States)

Raji, Jennifer; Atkinson, Carter T.

2013-01-01

This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa

DEFF Research Database (Denmark)

Heller, R; Okello, J B A; Siegismund, H

2010-01-01

populations, the level of genetic differentiation found here is comparable to that among pan-African populations. Overall, correlations between conservancy area and indices of genetic diversity suggest buffalo populations inhabiting small parks are showing signs of genetic erosion, stressing the need for more......The Cape buffalo (Syncerus caffer caffer) is one of the dominant and most widespread herbivores in sub-Saharan Africa. High levels of genetic diversity and exceptionally low levels of population differentiation have been found in the Cape buffalo compared to other African savannah ungulates...... active management of such populations. Our findings raise concerns about the future of other African savannah ungulates with lower population sizes and inferior dispersal capabilities compared with the buffalo....

An experimental study of strong reciprocity in bacteria.

Science.gov (United States)

Inglis, R Fredrik; West, Stuart; Buckling, Angus

2014-02-01

Strong reciprocity, whereby cooperators punish non-cooperators, may help to explain the evolutionary success of cooperative behaviours. However, theory suggests that selection for strong reciprocity can depend upon tight genetic linkage between cooperation and punishment, to avoid the strategy being outcompeted by non-punishing cooperators. We tested this hypothesis using experimental populations of the bacterium Pseudomonas aeruginosa, which cooperate by producing iron-scavenging siderophores and, in this context, punish non-cooperators with toxins. Consistent with theory, we show that cooperative punishers can indeed invade cheats, but only when the traits are tightly linked. These results emphasize that punishment is only likely to be favoured when the punishment itself leads to a direct or indirect fitness benefit to the actor.

Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

Directory of Open Access Journals (Sweden)

Reim Stefanie

2016-06-01

Full Text Available In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR and chloroplast single nucleotide polymorphism (cpSNP. In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA. The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

Probabilistic models for neural populations that naturally capture global coupling and criticality.

Science.gov (United States)

Humplik, Jan; Tkačik, Gašper

2017-09-01

Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system's state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.

A Nightmare for Males? A Maternally Transmitted Male-Killing Bacterium and Strong Female Bias in a Green Lacewing Population.

Directory of Open Access Journals (Sweden)

Masayuki Hayashi

Full Text Available For maternally transmitted microbes, a female-biased host sex ratio is of reproductive advantage. Here we found a strong female bias in a field population of the green lacewing, Mallada desjardinsi (Insecta; Neuroptera. This bias was attributed to the predominance of individuals harboring a maternally inherited male-killing bacterium that was phylogenetically closely related to the plant-pathogenic Spiroplasma phoeniceum and Spiroplasma kunkelii. Among 35 laboratory-reared broods produced by wild-caught females, 21 broods (60%-all infected with Spiroplasma-consisted of only females (940 individuals. Among 14 broods consisting of both males and females (516 and 635 individuals, respectively, 4 broods were doubly infected with Spiroplasma and Rickettsia, 6 broods were singly infected with Rickettsia, and 3 broods were uninfected (remaining one brood was unknown. Mortality during embryonic and larval development was prominent in all-female broods but not in normal sex ratio broods. Following antibiotic treatment on all-female broods, mortality was significantly reduced and the sex ratio was restored to 1:1. Strong expression and high prevalence of this male-killer is remarkable considering its low density (~10-5-10-4 cells per host mitochondrial gene copy based on quantitative PCR. In addition, a bacterium closely related to Rickettsia bellii was present in 25 of 34 broods (73.5%, irrespective of the sex ratio, with the infection density comparable to other cases of endosymbiosis (~10-2-10-1 cells per mitochondrial gene copy. Higher density of Rickettsia than Spiroplasma was also demonstrated by electron microscopy which visualized both Spiroplasma-like cells and Rickettsia-like cells inside and outside the ovarian cells.

Surveys in differential-algebraic equations IV

CERN Document Server

Reis, Timo

2017-01-01

The present volume comprises survey articles on various fields of Differential-Algebraic Equations (DAEs) which have widespread applications in controlled dynamical systems, especially in mechanical and electrical engineering and a strong relation to (ordinary) differential equations. The individual chapters provide reviews, presentations of the current state of research and new concepts in - History of DAEs - DAE aspects of mechanical multibody systems - Model reduction of DAEs - Observability for DAEs - Numerical Analysis for DAEs The results are presented in an accessible style, making this book suitable not only for active researchers but also for graduate students (with a good knowledge of the basic principles of DAEs) for self-study.

Surveys in differential-algebraic equations III

CERN Document Server

Reis, Timo

2015-01-01

The present volume comprises survey articles on various fields of Differential-Algebraic Equations (DAEs), which have widespread applications in controlled dynamical systems, especially in mechanical and electrical engineering and a strong relation to (ordinary) differential equations. The individual chapters provide reviews, presentations of the current state of research and new concepts in - Flexibility of DAE formulations - Reachability analysis and deterministic global optimization - Numerical linear algebra methods - Boundary value problems The results are presented in an accessible style, making this book suitable not only for active researchers but also for graduate students (with a good knowledge of the basic principles of DAEs) for self-study.