ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

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Velimir Gayevskiy

Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

Science.gov (United States)

Artzy-Randrup, Yael; Rorick, Mary M; Day, Karen; Chen, Donald; Dobson, Andrew P; Pascual, Mercedes

2012-01-01

The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity. DOI: http://dx.doi.org/10.7554/eLife.00093.001 PMID:23251784

Issues for Agricultural Extension Policy: Structures and Institutional ...

African Journals Online (AJOL)

This paper examined issues pertaining to structures and institutional arrangement for agricultural extension policy. It highlighted the broad objectives of the new policy thrust in agriculture in Nigeria, and identified sub-policies that were expected to facilitate growth of the agricultural sector of the economy. Agricultural ...

Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans.

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Eric A Lewallen

Full Text Available Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266. AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001. A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001, a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic

Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans)

Science.gov (United States)

Lewallen, Eric A.; Bohonak, Andrew J.; Bonin, Carolina A.; van Wijnen, Andre J.; Pitman, Robert L.; Lovejoy, Nathan R.

2016-01-01

Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps) from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266). AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001). A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001), a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic range of the

An age-structured extension to the vectorial capacity model.

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Vasiliy N Novoseltsev

Full Text Available Vectorial capacity and the basic reproductive number (R(0 have been instrumental in structuring thinking about vector-borne pathogen transmission and how best to prevent the diseases they cause. One of the more important simplifying assumptions of these models is age-independent vector mortality. A growing body of evidence indicates that insect vectors exhibit age-dependent mortality, which can have strong and varied affects on pathogen transmission dynamics and strategies for disease prevention.Based on survival analysis we derived new equations for vectorial capacity and R(0 that are valid for any pattern of age-dependent (or age-independent vector mortality and explore the behavior of the models across various mortality patterns. The framework we present (1 lays the groundwork for an extension and refinement of the vectorial capacity paradigm by introducing an age-structured extension to the model, (2 encourages further research on the actuarial dynamics of vectors in particular and the relationship of vector mortality to pathogen transmission in general, and (3 provides a detailed quantitative basis for understanding the relative impact of reductions in vector longevity compared to other vector-borne disease prevention strategies.Accounting for age-dependent vector mortality in estimates of vectorial capacity and R(0 was most important when (1 vector densities are relatively low and the pattern of mortality can determine whether pathogen transmission will persist; i.e., determines whether R(0 is above or below 1, (2 vector population growth rate is relatively low and there are complex interactions between birth and death that differ fundamentally from birth-death relationships with age-independent mortality, and (3 the vector exhibits complex patterns of age-dependent mortality and R(0 ∼ 1. A limiting factor in the construction and evaluation of new age-dependent mortality models is the paucity of data characterizing vector mortality

An Age-Structured Extension to the Vectorial Capacity Model

Science.gov (United States)

Novoseltsev, Vasiliy N.; Michalski, Anatoli I.; Novoseltseva, Janna A.; Yashin, Anatoliy I.; Carey, James R.; Ellis, Alicia M.

2012-01-01

Background Vectorial capacity and the basic reproductive number (R0) have been instrumental in structuring thinking about vector-borne pathogen transmission and how best to prevent the diseases they cause. One of the more important simplifying assumptions of these models is age-independent vector mortality. A growing body of evidence indicates that insect vectors exhibit age-dependent mortality, which can have strong and varied affects on pathogen transmission dynamics and strategies for disease prevention. Methodology/Principal Findings Based on survival analysis we derived new equations for vectorial capacity and R0 that are valid for any pattern of age-dependent (or age–independent) vector mortality and explore the behavior of the models across various mortality patterns. The framework we present (1) lays the groundwork for an extension and refinement of the vectorial capacity paradigm by introducing an age-structured extension to the model, (2) encourages further research on the actuarial dynamics of vectors in particular and the relationship of vector mortality to pathogen transmission in general, and (3) provides a detailed quantitative basis for understanding the relative impact of reductions in vector longevity compared to other vector-borne disease prevention strategies. Conclusions/Significance Accounting for age-dependent vector mortality in estimates of vectorial capacity and R0 was most important when (1) vector densities are relatively low and the pattern of mortality can determine whether pathogen transmission will persist; i.e., determines whether R0 is above or below 1, (2) vector population growth rate is relatively low and there are complex interactions between birth and death that differ fundamentally from birth-death relationships with age-independent mortality, and (3) the vector exhibits complex patterns of age-dependent mortality and R0∼1. A limiting factor in the construction and evaluation of new age-dependent mortality models is the

Extensive Air Showers with unusual structure

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Beznosko Dmitriy

2017-01-01

Full Text Available A total of 23500 Extensive Air Showers (EAS with energies above ∼ 1016 eV have been detected during the ∼3500 hours of the Horizon-T (HT detectors system operations before Aug. 2016. Among these EAS, more than a thousand had an unusual spatial and temporary structure that showed pulses with several maxima (modals or modes from several detection points of the HT at the same time. These modes are separated in time from each other starting from tens to thousands of ns. These EAS have been called multi-modal. Analysis shows that the multi-modal EAS that have been detected by Horizon-T have the following properties: 1. Multi-modal EAS have energy above ∼1017 eV. 2. Pulses with several modes are located at large distances from the EAS axis. An overview of the collected data will be provided. General comments about the unusual structure of the multi-modal EAS will be presented.

Population structure and adaptation in fishes

DEFF Research Database (Denmark)

Limborg, Morten

Marine fishes represent a valuable resource for the global economy and food consumption. Accordingly, many species experience high levels of exploitation necessitating effective management plans. However, long term sustainability may be jeopardized from insufficient knowledge about intra-specific......Marine fishes represent a valuable resource for the global economy and food consumption. Accordingly, many species experience high levels of exploitation necessitating effective management plans. However, long term sustainability may be jeopardized from insufficient knowledge about intra......-specific population structure and adaptive divergence. The large population sizes and high migration rates common to most marine fishes impede the differentiating effect of genetic drift, having led to expectations of no population structure and that the occurrence of local adaptation should be rare in these species....... Comprehensive genetic analyses on the small pelagic fish European sprat (Sprattus sprattus) revealed significant population structure throughout its distribution with an overall pattern of reduced connectivity across environmental transition zones. Population structure reflected both historical separations over...

Colony social organization and population genetic structure of an introduced population of formosan subterranean termite from New Orleans, Louisiana.

Science.gov (United States)

Husseneder, Claudia; Messenger, Matthew T; Su, Nan-Yao; Grace, J Kenneth; Vargo, Edward L

2005-10-01

The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive species in many parts of the world, including the U.S. mainland. The reasons for its invasive success may have to do with the flexible social and spatial organization of colonies. We investigated the population and breeding structure of 14 C. formosanus colonies in Louis Armstrong Park, New Orleans, LA. This population has been the focus of extensive study for many years, providing the opportunity to relate aspects of colony breeding structure to previous findings on colony characteristics such as body weight and number of workers, wood consumption, and intercolony aggression. Eight colonies were headed by a single pair of outbred reproductives (simple families), whereas six colonies were headed by low numbers of multiple kings and/or queens that were likely the neotenic descendants of the original colony (extended families). Within the foraging area of one large extended family colony, we found genetic differentiation among different collection sites, suggesting the presence of separate reproductive centers. No significant difference between simple family colonies and extended family colonies was found in worker body weight, soldier body weight, foraging area, population size, or wood consumption. However, level of inbreeding within colonies was negatively correlated with worker body weight and positively correlated with wood consumption. Also, genetic distance between colonies was positively correlated with aggression levels, suggesting a genetic basis to nestmate discrimination cues in this termite population. No obvious trait associated with colony reproductive structure was found that could account for the invasion success of this species.

Genetic structure of Suillus luteus populations in heavy metal polluted and nonpolluted habitats.

Science.gov (United States)

Muller, Ludo A H; Vangronsveld, Jaco; Colpaert, Jan V

2007-11-01

The genetic structure of populations of the ectomycorrhizal basidiomycete Suillus luteus in heavy metal polluted and nonpolluted areas was studied. Sporocarps were collected at nine different locations and genotyped at four microsatellite loci. Six of the sampling sites were severely contaminated with heavy metals and were dominated by heavy metal-tolerant individuals. Considerable genetic diversity was found within the geographical subpopulations, but no reduction of the genetic diversity, current or historic, was observed in subpopulations inhabiting polluted soils. The genetic differentiation between the geographical subpopulations was low, and no evidence for clustering of subpopulations from polluted soils vs. subpopulations from nonpolluted soils was found. These results indicate that heavy metal pollution has a limited effect on the genetic structure of S. luteus populations, and this may be due to the high frequency of sexual reproduction and extensive gene flow in S. luteus, which allows rapid evolution of the tolerance trait while maintaining high levels of genetic diversity.

LOOS: an extensible platform for the structural analysis of simulations.

Science.gov (United States)

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Structural stability of nonlinear population dynamics.

Science.gov (United States)

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Structural stability of nonlinear population dynamics

Science.gov (United States)

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Population activity structure of excitatory and inhibitory neurons.

Science.gov (United States)

Bittner, Sean R; Williamson, Ryan C; Snyder, Adam C; Litwin-Kumar, Ashok; Doiron, Brent; Chase, Steven M; Smith, Matthew A; Yu, Byron M

2017-01-01

Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure.

Population activity structure of excitatory and inhibitory neurons.

Directory of Open Access Journals (Sweden)

Sean R Bittner

Full Text Available Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure.

Population activity structure of excitatory and inhibitory neurons

Science.gov (United States)

Doiron, Brent

2017-01-01

Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure. PMID:28817581

Extensive genetic divergence among Diptychus maculatus populations in northwest China

Science.gov (United States)

Meng, Wei; Yang, Tianyan; Hai, Sa; Ma, Yanwu; Cai, Lingang; Ma, Xufa; Gao, Tianxiang; Guo, Yan

2015-05-01

D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity ( h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences ( k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other ( P<0.01). The largest F st value was between Yurungkash River population and Muzat River population, while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.

Coal handling system structural analysis for modifications or plant life extension

International Nuclear Information System (INIS)

Dufault, A.; Weider, F.; Doyle, P.

1989-01-01

One neglected aspect of plant modification or life extension is the extent to which previous projects may have affected the integrity of existing structures. During the course of a project to backfit fire protection facilities to existing coal handling systems, it was found that past modifications had added loads to existing coal handling structures which exceeded the available design margin. This paper describes the studies that discovered the original problem areas, as well as the detailed analysis and design considerations used to repair these structures

On Hierarchical Extensions of Large-Scale 4-regular Grid Network Structures

DEFF Research Database (Denmark)

Pedersen, Jens Myrup; Patel, A.; Knudsen, Thomas Phillip

2004-01-01

dependencies between the number of nodes and the distances in the structures. The perfect square mesh is introduced for hierarchies, and it is shown that applying ordered hierarchies in this way results in logarithmic dependencies between the number of nodes and the distances, resulting in better scaling...... structures. For example, in a mesh of 391876 nodes the average distance is reduced from 417.33 to 17.32 by adding hierarchical lines. This is gained by increasing the number of lines by 4.20% compared to the non-hierarchical structure. A similar hierarchical extension of the torus structure also results...

Calculating evolutionary dynamics in structured populations.

Directory of Open Access Journals (Sweden)

Charles G Nathanson

2009-12-01

Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

Visualising the demographic factors which shape population age structure

Directory of Open Access Journals (Sweden)

Tom Wilson

2016-09-01

Full Text Available Background: The population pyramid is one of the most popular tools for visualising population age structure. However, it is difficult to discern from the diagram the relative effects of different demographic components on the size of age-specific populations, making it hard to understand exactly how a population's age structure is formed. Objective: The aim of this paper is to introduce a type of population pyramid which shows how births, deaths, and migration have shaped a population's age structure. Methods: Births, deaths, and population data were obtained from the Human Mortality Database and the Australian Bureau of Statistics. A variation on the conventional population pyramid, termed here a components-of-change pyramid, was created. Based on cohort population accounts, it illustrates how births, deaths, and net migration have created the population of each age group. A simple measure which summarises the impact of net migration on age structure is also suggested. Results: Example components-of-change pyramids for several countries and subnational regions are presented, which illustrate how births, deaths, and net migration have fashioned current population age structures. The influence of migration is shown to vary greatly between populations. Conclusions: The new type of pyramid aids interpretation of a population's age structure and helps to understand its demographic history over the last century.

Structured population dynamics: continuous size and discontinuous stage structures.

Science.gov (United States)

Buffoni, Giuseppe; Pasquali, Sara

2007-04-01

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

Structured population models in biology and epidemiology

CERN Document Server

Ruan, Shigui

2008-01-01

This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

The population genomics of begomoviruses: global scale population structure and gene flow

Directory of Open Access Journals (Sweden)

Prasanna HC

2010-09-01

Full Text Available Abstract Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

Science.gov (United States)

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or

Stability patterns for a size-structured population model and its stage-structured counterpart

DEFF Research Database (Denmark)

Zhang, Lai; Pedersen, Michael; Lin, Zhigui

2015-01-01

In this paper we compare a general size-structured population model, where a size-structured consumer feeds upon an unstructured resource, to its simplified stage-structured counterpart in terms of equilibrium stability. Stability of the size-structured model is understood in terms of an equivale...... to the population level....

Population structure and recruitment of penaeid shrimps in ...

African Journals Online (AJOL)

Population structure and recruitment of penaeid shrimps in mozambique. ... This study characterizes the population structure and identifies nursery areas and recruitment seasons of penaeid shrimps in the ... AJOL African Journals Online.

Population Structure of West Greenland Narwhals

DEFF Research Database (Denmark)

Riget, F.; Dietz, R.; Møller, P.

The hypothesis that different populations of narwhals in the West Greenland area exist has been tested by different biomarkers (metal and organochlorine concentrations, stable isotopes and DNA). Samples of muscle, liver, kidney, blubber and skin tissues of narwhals from West Greenland have been...... isotopes could not support the population structure with two West Greenland populations suggested by the genetic study....

Phylogeography, population structure and evolution of coral-eating butterflyfishes (Family Chaetodontidae, genus Chaetodon , subgenus Corallochaetodon )

KAUST Repository

Waldrop, Ellen

2016-01-11

Aim This study compares the phylogeography, population structure and evolution of four butterflyfish species in the Chaetodon subgenus Corallochaetodon, with two widespread species (Indian Ocean – C. trifasciatus and Pacific Ocean – C. lunulatus), and two species that are largely restricted to the Red Sea (C. austriacus) and north-western (NW) Indian Ocean (C. melapterus). Through extensive geographical coverage of these taxa, we seek to resolve patterns of genetic diversity within and between closely related butterflyfish species in order to illuminate biogeographical and evolutionary processes. Location Red Sea, Indian Ocean and Pacific Ocean. Methods A total of 632 individuals from 24 locations throughout the geographical ranges of all four members of the subgenus Corallochaetodon were sequenced using a 605 bp fragment (cytochrome b) of mtDNA. In addition, 10 microsatellite loci were used to assess population structure in the two widespread species. Results Phylogenetic reconstruction indicates that the Pacific Ocean C. lunulatus diverged from the Indian Ocean C. trifasciatus approximately 3 Ma, while C. melapterus and C. austriacus comprise a cluster of shared haplotypes derived from C. trifasciatus within the last 0.75 Myr. The Pacific C. lunulatus had significant population structure at peripheral locations on the eastern edge of its range (French Polynesia, Johnston Atoll, Hawai\\'i), and a strong break between two ecoregions of the Hawaiian Archipelago. The Indian Ocean C. trifasciatus showed significant structure only at the Chagos Archipelago in the central Indian Ocean, and the two range-restricted species showed no population structure but evidence of recent population expansion. Main conclusions Patterns of endemism and genetic diversity in Corallochaetodon butterflyfishes have been shaped by (1) Plio-Pleistocene sea level changes that facilitated evolutionary divergences at biogeographical barriers between Indian and Pacific Oceans, and the Indian

Population structure of the Classic period Maya.

Science.gov (United States)

Scherer, Andrew K

2007-03-01

This study examines the population structure of Classic period (A.D. 250-900) Maya populations through analysis of odontometric variation of 827 skeletons from 12 archaeological sites in Mexico, Guatemala, Belize, and Honduras. The hypothesis that isolation by distance characterized Classic period Maya population structure is tested using Relethford and Blangero's (Hum Biol 62 (1990) 5-25) approach to R matrix analysis for quantitative traits. These results provide important biological data for understanding ancient Maya population history, particularly the effects of the competing Tikal and Calakmul hegemonies on patterns of lowland Maya site interaction. An overall F(ST) of 0.018 is found for the Maya area, indicating little among-group variation for the Classic Maya sites tested. Principal coordinates plots derived from the R matrix analysis show little regional patterning in the data, though the geographic outliers of Kaminaljuyu and a pooled Pacific Coast sample did not cluster with the lowland Maya sites. Mantel tests comparing the biological distance matrix to a geographic distance matrix found no association between genetic and geographic distance. In the Relethford-Blangero analysis, most sites possess negative or near-zero residuals, indicating minimal extraregional gene flow. The exceptions were Barton Ramie, Kaminaljuyu, and Seibal. A scaled R matrix analysis clarifies that genetic drift is a consideration for understanding Classic Maya population structure. All results indicate that isolation by distance does not describe Classic period Maya population structure. (c) 2006 Wiley-Liss, Inc.

Dominance and population structure of freshwater crabs ...

African Journals Online (AJOL)

To understand how this would affect wild populations we also investigated the population structure (sex ratio, size distribution, density and population growth) of a wild population. Using Landau's index of linearity (h) we found three captive groups of P. perlatus to show moderate linearity, i.e. h = 0.9; 0.81 and 0.83.

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.

Dynamical community structure of populations evolving on genotype networks

International Nuclear Information System (INIS)

Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

2015-01-01

Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.

Science.gov (United States)

Raghavan, Chitra; Mauleon, Ramil; Lacorte, Vanica; Jubay, Monalisa; Zaw, Hein; Bonifacio, Justine; Singh, Rakesh Kumar; Huang, B Emma; Leung, Hei

2017-06-07

Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations. Copyright © 2017 Raghavan et al.

Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population

Directory of Open Access Journals (Sweden)

Chitra Raghavan

2017-06-01

Full Text Available Multi-parent Advanced Generation Intercross (MAGIC populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL mapping. In this study, 1316 S6:8 indica MAGIC (MI lines and the eight founders were sequenced using Genotyping by Sequencing (GBS. As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height, physical (grain length and grain width and cooking properties (amylose content of the rice grain, abiotic stress (submergence tolerance, and biotic stress (brown spot disease were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations.

Modeling evolutionary games in populations with demographic structure

DEFF Research Database (Denmark)

Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette

2015-01-01

interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals...

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

Science.gov (United States)

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

Structural strengthening of rocket nozzle extension by means of laser metal deposition

Science.gov (United States)

Honoré, M.; Brox, L.; Hallberg, M.

2012-03-01

Commercial space operations strive to maximize the payload per launch in order to minimize the costs of each kg launched into orbit; this yields demand for ever larger launchers with larger, more powerful rocket engines. Volvo Aero Corporation in collaboration with Snecma and Astrium has designed and tested a new, upgraded Nozzle extension for the Vulcain 2 engine configuration, denoted Vulcain 2+ NE Demonstrator The manufacturing process for the welding of the sandwich wall and the stiffening structure is developed in close cooperation with FORCE Technology. The upgrade is intended to be available for future development programs for the European Space Agency's (ESA) highly successful commercial launch vehicle, the ARIANE 5. The Vulcain 2+ Nozzle Extension Demonstrator [1] features a novel, thin-sheet laser-welded configuration, with laser metal deposition built-up 3D-features for the mounting of stiffening structure, flanges and for structural strengthening, in order to cope with the extreme load- and thermal conditions, to which the rocket nozzle extension is exposed during launch of the 750 ton ARIANE 5 launcher. Several millimeters of material thickness has been deposited by laser metal deposition without disturbing the intricate flow geometry of the nozzle cooling channels. The laser metal deposition process has been applied on a full-scale rocket nozzle demonstrator, and in excess of 15 kilometers of filler wire has been successfully applied to the rocket nozzle. The laser metal deposition has proven successful in two full-throttle, full-scale tests, firing the rocket engine and nozzle in the ESA test facility P5 by DLR in Lampoldshausen, Germany.

Training set optimization under population structure in genomic selection.

Science.gov (United States)

Isidro, Julio; Jannink, Jean-Luc; Akdemir, Deniz; Poland, Jesse; Heslot, Nicolas; Sorrells, Mark E

2015-01-01

Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.

Human population structure detection via multilocus genotype clustering

Directory of Open Access Journals (Sweden)

Starmer Joshua

2007-06-01

Full Text Available Abstract Background We describe a hierarchical clustering algorithm for using Single Nucleotide Polymorphism (SNP genetic data to assign individuals to populations. The method does not assume Hardy-Weinberg equilibrium and linkage equilibrium among loci in sample population individuals. Results We show that the algorithm can assign sample individuals highly accurately to their corresponding ethnic groups in our tests using HapMap SNP data and it is also robust to admixed populations when tested with Perlegen SNP data. Moreover, it can detect fine-scale population structure as subtle as that between Chinese and Japanese by using genome-wide high-diversity SNP loci. Conclusion The algorithm provides an alternative approach to the popular STRUCTURE program, especially for fine-scale population structure detection in genome-wide association studies. This is the first successful separation of Chinese and Japanese samples using random SNP loci with high statistical support.

Genetic diversity and population structure of Chinese honeybees ...

African Journals Online (AJOL)

Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

Genetic structure of a unique admixed population: implications for medical research.

Science.gov (United States)

Patterson, Nick; Petersen, Desiree C; van der Ross, Richard E; Sudoyo, Herawati; Glashoff, Richard H; Marzuki, Sangkot; Reich, David; Hayes, Vanessa M

2010-02-01

STATEMENT: In naming population groups, we think a chief aim is to use terms that the group members use themselves, or find familiar and comfortable. The terms used in this manuscript to describe populations are as historically correct as possible and are chosen so as not to offend any population group. Two of the authors (DCP and REvdR) belong to the Coloured population, with one of the authors (REvdR) having contributed extensively to current literature on the history of the Coloured people of South Africa and served as Vice-President of the South African Institute of Race Relations. According to the 2001 South African census (http://www.statssa.gov.za/census01/HTML/CInBrief/CIB2001.pdf), "Statistics South Africa continues to classify people by population group, in order to monitor progress in moving away from the apartheid-based discrimination of the past. However, membership of a population group is now based on self-perception and self-classification, not on a legal definition. Five options were provided on the questionnaire, Black African, Coloured, Indian or Asian, White and Other. Responses in the category 'Other' were very few and were therefore imputed". We have elected to use the term Bushmen rather than San to refer to the hunter-gatherer people of Southern Africa. Although they have no collective name for themselves, this decision was based on the term Bushmen (or Bossiesman) being the more familiar to the communities themselves, while the term San is the more accepted academic classification. Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected

Population structure of a widespread species under balancing selection: the case of Arbutus unedo L.

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Xabier eSantiso

2016-01-01

Full Text Available Arbutus unedo L. is an evergreen shrub with a circum-Mediterranean distribution that also reaches the Eurosiberian region in northern Iberia, Atlantic France, and a disjunct population in southern Ireland. Due to the variety of climatic conditions across its distribution range, the populations of A. unedo were expected to display local adaptation. Conversely, common garden experiments revealed that diverse genotypes from a range of provenances produce similar phenotypes through adaptive plasticity, suggesting the action of stabilizing selection across its climatically heterogeneous range. Nonetheless, since an uniform response might also result from extensive gene flow, we have inferred the population structure of A. unedo and assessed whether its extended and largely one-dimensional range influences gene flow with the help of AFLP genotypes for 491 individuals from 19 populations covering the whole range of the species. As we had anticipated, gene flow is restricted in A. unedo, providing further support to the hypothesis that stabilizing selection is the most likely explanation for the homogeneous phenotypes along the range. The Euro-Siberian populations were not particularly isolated from the Mediterranean. Instead, there was a distinct genetic divide between the populations around the Mediterranean Sea and those sampled along Atlantic coasts from northern Africa up to Ireland. This genetic structure suggests the action of historic rather than biogeographic factors as it seems consistent with a scenario of independent glacial refugia in the Atlantic and Mediterranean portions of the range of A. unedo. Genetic exchange was likewise restricted within each set of populations. Nevertheless, IBD was stronger, and FST increased faster with distance, along the Atlantic, suggesting that gene flow might be larger among Mediterranean populations. Genetic diversity was significantly lower in NW Iberia and Ireland than in other populations whereas

Population Structure of a Widespread Species under Balancing Selection: The Case of Arbutus unedo L.

Science.gov (United States)

Santiso, Xabier; Lopez, Lua; Retuerto, Rubén; Barreiro, Rodolfo

2015-01-01

Arbutus unedo L. is an evergreen shrub with a circum-Mediterranean distribution that also reaches the Eurosiberian region in northern Iberia, Atlantic France, and a disjunct population in southern Ireland. Due to the variety of climatic conditions across its distribution range, the populations of A. unedo were expected to display local adaptation. Conversely, common garden experiments revealed that diverse genotypes from a range of provenances produce similar phenotypes through adaptive plasticity, suggesting the action of stabilizing selection across its climatically heterogeneous range. Nonetheless, since a uniform response might also result from extensive gene flow, we have inferred the population structure of A. unedo and assessed whether its extended and largely one-dimensional range influences gene flow with the help of AFLP genotypes for 491 individuals from 19 populations covering the whole range of the species. As we had anticipated, gene flow is restricted in A. unedo, providing further support to the hypothesis that stabilizing selection is the most likely explanation for the homogeneous phenotypes along the range. The Euro-Siberian populations were not particularly isolated from the Mediterranean. Instead, there was a distinct genetic divide between the populations around the Mediterranean Sea and those sampled along Atlantic coasts from northern Africa up to Ireland. This genetic structure suggests the action of historic rather than biogeographic factors as it seems consistent with a scenario of independent glacial refugia in the Atlantic and Mediterranean portions of the range of A. unedo. Genetic exchange was likewise restricted within each set of populations. Nevertheless, isolation-by-distance (IBD) was stronger, and F ST increased faster with distance, along the Atlantic, suggesting that gene flow might be larger among Mediterranean populations. Genetic diversity was significantly lower in NW Iberia and Ireland than in other populations whereas

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

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Martina Temunović

Full Text Available Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM. We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Genetic diversity and population structure in the Leishmania guyanensis vector Lutzomyia anduzei (Diptera, Psychodidae) from the Brazilian Amazon.

Science.gov (United States)

Scarpassa, Vera Margarete; Figueiredo, Adrya da Silva; Alencar, Ronildo Baiatone

2015-04-01

Lutzomyia (Nyssomyia) anduzei has been recognized as a secondary vector of Leishmania guyanensis in the Brazilian Amazon region. Since L. anduzei is anthropophilic, co-exists in areas of high leishmaniasis transmission and has been found infected with L. guyanensis, the understanding of the vector population structure and of the process responsible for it is paramount to the vector management and control efforts. In this study we analyzed 74 and 67 sequences of the COI and Cytb loci, respectively, from mitochondrial DNA, aiming to estimate the intra-population genetic variability and population structure in six L. anduzei samples from the Brazilian Amazon region. For COI, we found 58 haplotypes, low to high (FST=0.0310-0.4128) and significant (P=0.0033) genetic structure, and reduced gene flow among populations. The haplotype network yielded many reticulations that likely resulted from hypervariability in the locus. For Cytb, we observed 27 haplotypes, low to moderate (FST=0.0077-0.1954) and nonsignificant (P>0.05) genetic structure for the majority of comparisons and extensive gene flow among populations, in line with the haplotypes network data. AMOVA analysis indicated that most of the variation occurred within populations (83.41%, 90.94%); nevertheless, there were significant differences (ΦST=0.0906-0.1659; P=0.00098; P=0.00000) among them for both loci. The Mantel test showed that the genetic structure is not associated to an isolation-by-distance (IBD) model in either of both loci. These data suggest that L. anduzei is genetically very diverse. The genetic structure lacking IBD may be due to adaptation to local habitats and the low dispersal capacity of the sandflies, and both could lead to population fragmentation and geographic isolation. These findings have important implications for epidemiology, surveillance and vector control and may be a first step in understanding the evolutionary history of this species. Copyright © 2015 Elsevier B.V. All rights

Competition in size-structured populations: mechanisms inducing cohort formation and population cycles

NARCIS (Netherlands)

de Roos, A.M.; Persson, L.

2003-01-01

In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and

A review of assessment and retrofitting of structures for plant life extension (PLEX) programme

International Nuclear Information System (INIS)

Samota, A.; Verma, U.S.P.; Tilak, M.M.

1994-01-01

Assessment of the life of existing civil engineering structures for the plant life extension programme has to be made considering various factors such as strength, deterioration, environmental impact particularly with regard to radiation field, etc. which need to be evaluated very carefully. Generally, it is considered that initial design usually caters for a period of around 40 years, though structural failures have been reported even at a much younger stage due to deficiency in design and construction. In the context of nuclear power plant when the initial license is given for a period 30-40 years, it becomes necessary to evaluate the health of the various structures particularly while applying for a license for the extension of plant life. The present paper discuss the various issues connected with the evaluation of the future life of an existing structure in terms of strength and change in its property particularly when the structure is exposed to radiation. The various effects with regard to ageing and radiation exposure and the destructive and non-destructive tests which need to be carried out are discussed in detail. (author). 8 refs., 4 figs

Plasmodium vivax Diversity and Population Structure across Four Continents.

Science.gov (United States)

Koepfli, Cristian; Rodrigues, Priscila T; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y M; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U; Felger, Ingrid

2015-01-01

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999-2008. Diversity was highest in South-East Asia (mean allelic richness 10.0-12.8), intermediate in the South Pacific (8.1-9.9) Madagascar and Sudan (7.9-8.4), and lowest in South America and Central Asia (5.5-7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60-80% in Latin American populations, suggesting that typing of 2-6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11-0.16) between South American and all other populations, and lowest (0.04-0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

Population structure of Han nationality in Central-Southern China.

Science.gov (United States)

Liu, Qiu-Ling; Chen, Ye-Fei; He, Xin; Shi, Yan-Wei; Wu, Wei-Wei; Zhao, Hu; Lu, De-Jian

2017-07-01

Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a F st value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing. Copyright © 2017. Published by Elsevier B.V.

Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

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Jiali Zhao

Full Text Available We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1 determine the level of genetic diversity across the studied regions; (2 explore the likely origins of invasive populations in China; and (3 investigate whether there is the evidence of multiple introductions into China.We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China.We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F IS or population differentiation (F ST. Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.

Genetic diversity and population structure of sweet cassava using ...

African Journals Online (AJOL)

The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

Population genetic structure in wild and aquaculture populations of Hemibarbus maculates inferred from microsatellites markers

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Linlin Li

2017-03-01

Full Text Available The objective of this study was to investigate 4 aquaculture populations Shanghai (SH, Hangzhou (HZ, Kaihua (KH and Xianju (XJ and one wild population Yingshan (YS of spotted barbell (Hemibarbus maculates to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

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Chunping Liu

Full Text Available Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE, whereas it has a scattered and patchy distribution in South China (SC. In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM. Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278 among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

Science.gov (United States)

Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

Science.gov (United States)

Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

A general modeling framework for describing spatially structured population dynamics

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Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

2017-01-01

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

Effects of demographic structure on key properties of stochastic density-independent population dynamics.

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Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

2012-12-01

The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

Agricultural Extension: Farm Extension Services in Australia, Britain and the United States.

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Williams, Donald B.

By analyzing the scope and structure of agricultural extension services in Australia, Great Britain, and the United States, this work attempts to set guidelines for measuring progress and guiding extension efforts. Extension training, agricultural policy, and activities of national, international, state, and provincial bodies are examined. The…

Coexistence of competing stage-structured populations.

KAUST Repository

Fujiwara, Masami

2011-10-05

This paper analyzes the stability of a coexistence equilibrium point of a model for competition between two stage-structured populations. In this model, for each population, competition for resources may affect any one of the following population parameters: reproduction, juvenile survival, maturation rate, or adult survival. The results show that the competitive strength of a population is affected by (1) the ratio of the population parameter influenced by competition under no resource limitation (maximum compensatory capacity) over the same parameter under a resource limitation due to competition (equilibrium rate) and (2) the ratio of interspecific competition over intraspecific competition; this ratio was previously shown to depend on resource-use overlap. The former ratio, which we define as fitness, can be equalized by adjusting organisms\\' life history strategies, thereby promoting coexistence. We conclude that in addition to niche differentiation among populations, the life history strategies of organisms play an important role in coexistence.

Inspection and mitigating measures for life extension of nuclear power plant containment structures

International Nuclear Information System (INIS)

Meyers, B.L.; Daye, M.A.

1989-01-01

The subject of life extension of nuclear power plants has drawn considerable attention during the last few years. Interest in life extension initiated because of both safety and economic reasons. A number of evaluations have been performed. The main thrust of earlier work was directed toward evaluating the factors causing aging, and defining degradation sites, degradation mechanism and failure modes. At present, attention is directed toward establishing the appropriate inspection programs suitable for each of the defined aging sites. Some components and aging sites are already subjected to routine inspection programs such as the surveillance of post-tensioning system and the integrated leak rate test (ILRT) of prestressed concrete and reinforced concrete containments. The aging process affects mechanical, electrical and structural components in all types of containments. This paper addresses the structural components of PWR containments only and presents examples of inspection approaches and describes methods to prevent further degradation of select sites

Pseudomonas aeruginosa Population Structure Revisited

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Pirnay, Jean-Paul; Bilocq, Florence; Pot, Bruno; Cornelis, Pierre; Zizi, Martin; Van Eldere, Johan; Deschaght, Pieter; Vaneechoutte, Mario; Jennes, Serge; Pitt, Tyrone; De Vos, Daniel

2009-01-01

At present there are strong indications that Pseudomonas aeruginosa exhibits an epidemic population structure; clinical isolates are indistinguishable from environmental isolates, and they do not exhibit a specific (disease) habitat selection. However, some important issues, such as the worldwide emergence of highly transmissible P. aeruginosa clones among cystic fibrosis (CF) patients and the spread and persistence of multidrug resistant (MDR) strains in hospital wards with high antibiotic pressure, remain contentious. To further investigate the population structure of P. aeruginosa, eight parameters were analyzed and combined for 328 unrelated isolates, collected over the last 125 years from 69 localities in 30 countries on five continents, from diverse clinical (human and animal) and environmental habitats. The analysed parameters were: i) O serotype, ii) Fluorescent Amplified-Fragment Length Polymorphism (FALFP) pattern, nucleotide sequences of outer membrane protein genes, iii) oprI, iv) oprL, v) oprD, vi) pyoverdine receptor gene profile (fpvA type and fpvB prevalence), and prevalence of vii) exoenzyme genes exoS and exoU and viii) group I pilin glycosyltransferase gene tfpO. These traits were combined and analysed using biological data analysis software and visualized in the form of a minimum spanning tree (MST). We revealed a network of relationships between all analyzed parameters and non-congruence between experiments. At the same time we observed several conserved clones, characterized by an almost identical data set. These observations confirm the nonclonal epidemic population structure of P. aeruginosa, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise. One of these clones is the renown and widespread MDR serotype O12 clone. On the other hand, we found no evidence for a widespread CF transmissible clone. All but one of the 43 analysed CF strains belonged to a ubiquitous P

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...

15 CFR 50.10 - Fee structure for special population censuses.

Science.gov (United States)

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned. To...

Population structure age of Paraná state between 1970 and 2010

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Eduardo de Pintor

2014-06-01

Full Text Available The theory of demographic transition began with an effort of Frank Notestein (1945 to understand the demographic changes that were occurring in Western Europe since the late nineteenth century. The demographic transition is the transition between two scenarios of population growth, which changes the age structure of the population. The aim of the article is to discuss the evolution of population structure age of Paraná state between 1970 and 2010. The changes in the age structure of the Paraná indicate a reduction in the share of young population and increasing aging population, an increase in the relative weight of the elderly population. Public policies on education, health, social security and labor market should consider the current change in the age structure. Thus, the aim of this study was to analyze the change in the age structure of the population of the state of Paraná. For this we used data Censuses of the Brazilian Institute of Geography and Statistics (IBGE on the age distribution of urban and rural Paraná and its Mesoregions. It was concluded that the change in structure occurs group widespread in all Mesoregions state. However, it occurs unevenly between urban and rural population.

Population genetic structure of Diaphorina citri Kuwayama (Hemiptera: Liviidae): host-driven genetic differentiation in China.

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Meng, Lixue; Wang, Yongmo; Wei, Wen-Hua; Zhang, Hongyu

2018-01-24

The Asian citrus psyllid Diaphorina citri Kuwayama is a major pest in citrus production, transmitting Candidatus Liberibacter asiaticus. It has spread widely across eastern and southern China. Unfortunately, little is known about the genetic diversity and population structure of D. citri, making pest control difficult. In this study, nine specifically developed SSR markers and three known mitochondrial DNA were used for population genetics study of D. citri using 225 samples collected from all 7 distribution regions in China. Based on the SSR data, D. citri was found highly diverse with a mean observed heterozygosity of 0.50, and three subgroups were structured by host plant: (i) Shatangju, NF mandarin and Ponkan; (ii) Murraya paniculata and Lemon; (iii) Citrus unshiu, Bingtangcheng, Summer orange and Navel. No significant genetic differences were found with mtDNA data. We suggested the host-associated divergence is likely to have occurred very recently. A unimodal distribution of paired differences, the negative and significant Tajima's D and Fu's F S parameters among mtDNA suggested a recent demographic expansion. The extensive citrus cultivation and increased suitable living habitat was recommended as a key for this expansion event.

Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis.

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Morgana Vighi

Full Text Available From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina and another off central Argentina (Peninsula Valdés. This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72 and from contemporary and more recent strandings occurring in central Argentina (n=53. Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

Assessing population genetic structure via the maximisation of genetic distance

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Toro Miguel A

2009-11-01

Full Text Available Abstract Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy

Distribution and population structure of North Atlantic harbour seals (Phoca vitulina

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Liselotte Andersen

2010-09-01

Full Text Available A review of the known geographical distribution and current knowledge on the genetic population structure of harbour seals (Phoca vitulina in the North Atlantic is presented. Based on a synthesis of the results fromfive different studies of neutral geneticmarkers (mtDNAand nuclear microsatellites, mainly twelve genetically distinct populations were identified in the North Atlantic: USA/Canada, Iceland, west coast of Norway, Ireland-Scotland, English east coast, Channel area, Wadden Sea, Limfjord, Skagerrak, Kattegat, West Baltic, and East Baltic. Most of the studies addressed the population structure at the regional level, while only a few addressed the structuring at a local level, i.e. within countries. Due to the limited number of studies conducted, the identified population units were considered preliminary andmore detailed, local studieswould probably reveal structuring on a finer scale. The choice of genetic markers, their properties, resolution in time and applicability in population structure studies is shortly discussed and compared to ecological methods used to delineate populations.

Effect of Population Structure Change on Carbon Emission in China

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Wen Guo

2016-03-01

Full Text Available This paper expanded the Logarithmic Mean Divisia Index (LMDI model through the introduction of urbanization, residents’ consumption, and other factors, and decomposed carbon emission changes in China into carbon emission factor effect, energy intensity effect, consumption inhibitory factor effect, urbanization effect, residents’ consumption effect, and population scale effect, and then explored contribution rates and action mechanisms of the above six factors on change in carbon emissions in China. Then, the effect of population structure change on carbon emission was analyzed by taking 2003–2012 as a sample period, and combining this with the panel data of 30 provinces in China. Results showed that in 2003–2012, total carbon emission increased by 4.2117 billion tons in China. The consumption inhibitory factor effect, urbanization effect, residents’ consumption effect, and population scale effect promoted the increase in carbon emissions, and their contribution ratios were 27.44%, 12.700%, 74.96%, and 5.90%, respectively. However, the influence of carbon emission factor effect (−2.54% and energy intensity effect (−18.46% on carbon emissions were negative. Population urbanization has become the main population factor which affects carbon emission in China. The “Eastern aggregation” phenomenon caused the population scale effect in the eastern area to be significantly higher than in the central and western regions, but the contribution rate of its energy intensity effect (−11.10 million tons was significantly smaller than in the central (−21.61 million tons and western regions (−13.29 million tons, and the carbon emission factor effect in the central area (−3.33 million tons was significantly higher than that in the eastern (−2.00 million tons and western regions (−1.08 million tons. During the sample period, the change in population age structure, population education structure, and population occupation structure

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

Science.gov (United States)

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

Phytophthora infestans population structure: A worldwide scale

International Nuclear Information System (INIS)

Cardenas, Martha; Danies, Giovanna; Tabima, Javier; Bernal, Adriana; Restrepo, Silvia

2012-01-01

Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of the pathogen's population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase) and Pep (Pep tidase), the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America, expanding it on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.

Phytophthora infestans population structure: a worldwide scale

Directory of Open Access Journals (Sweden)

Martha Cárdenas Toquica

2012-05-01

Full Text Available Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase and Pep (Peptidase, the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and the mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America expanding on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.

High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems

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Yin Li

2012-12-01

Full Text Available Abstract Background Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3 within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children. Results Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later. Conclusions Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.

Improving Disability Awareness among Extension Agents

Science.gov (United States)

Mahadevan, Lakshmi; Peterson, Rick L.; Grenwelge, Cheryl

2014-01-01

Increasing prevalence rates and legislative mandates imply that educators, parents, and Extension agents will need better tools and resources to meet the needs of special populations. The Texas A&M AgriLife Extension Service addresses this issue by using e-learning tools. Extension agents can take advantage of these courses to gain critical…

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.

Shallow Population Genetic Structures of Thread-sail Filefish ( Populations from Korean Coastal Waters

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M. Yoon

2012-02-01

Full Text Available Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076 and nucleotide diversities (0.014 to 0.019, and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107, support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05, and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23. These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

Science.gov (United States)

Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

2018-04-16

Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

Structure of the New England herring gull population

Science.gov (United States)

Kadlec, J.A.; Drury, W.H.

1968-01-01

Measurements of the rates of population increase, reproduction, and mortality together with an observed age ratio, were used to analyze the population of the Herring Gull in New England. Data from sporadic censuses prior to this study, aerial censuses by the authors, and National Audubon Society Christmas Bird Count indicated that the New England breeding population has been doubling every 12 to 15 years since the early 1900's. This increase has involved founding new colonies and expanding the breeding range There is evidence that 15 to 30% of the adults do not breed in any given year. Sixty-one productivity measurements on 43 islands from 1963 through 1966, involving almost 13,000 nests, showed that from 0.8 to 1.4 young/breeding pair/year is the usual range of rate of production. The age distribution in the population was determined by classifying Herring Gulls by plumage category on an aerial census of the coast from Tampico, Mexico, to Cape Sable, Nova Scotia. Of the 622,000 gulls observed, 68% were adults, 17% were second- and third-year birds, and 15% were first-year birds. Mortality rates derived from band recovery data were too high to be consistent with the observed rate of population growth, productivity, and age structure. Loss of bands increasing to the rate of about 20%/year 5 years after banding eliminates most of the discrepancy. The age structure and rate of population increase indicate a mortality rate of 4 to 9% for gulls 2 years old or older, compared with the 25 to 30% indicated by band recoveries. The population structure we have developed fits everything we have observed about Herring Gull population dynamics, except mortality based on band recoveries.

Kin groups and trait groups: population structure and epidemic disease selection.

Science.gov (United States)

Fix, A G

1984-10-01

A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of

The scale of population structure in Arabidopsis thaliana.

Directory of Open Access Journals (Sweden)

Alexander Platt

2010-02-01

Full Text Available The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

Structural Approaches to Sequence Evolution Molecules, Networks, Populations

CERN Document Server

Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

2007-01-01

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

Population structure and genetic diversity of Sudanese native chickens

African Journals Online (AJOL)

The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

Mapping population-based structural connectomes.

Science.gov (United States)

Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

2018-05-15

Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.

Familial identification: population structure and relationship distinguishability.

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Rohlfs, Rori V; Fullerton, Stephanie Malia; Weir, Bruce S

2012-02-01

With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

Familial identification: population structure and relationship distinguishability.

Directory of Open Access Journals (Sweden)

Rori V Rohlfs

2012-02-01

Full Text Available With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

Population Genetic Structure and Gene Flow Among Nigerian Goats ...

African Journals Online (AJOL)

Population Genetic structure in 200 indigenous goats sampled across four states from the South-Western and South Southern region of Nigeria was assessed using 7 microsatellite DNA markers. Observed Analysis of molecular genetic variation (AMOVA) was higher within populations (3.47) than among populations (1.84) ...

Population structure and expansion of kuruma shrimp ( Penaeus ...

African Journals Online (AJOL)

Sequence analyses on the specific intron from the elongation factor-1α gene were conducted to examine the population genetic structure and expansion of kuruma shrimp (Penaeus japonicus) off Taiwan. Five populations including 119 individuals were separately sampled from the north of East China Sea (ECS), west of ...

Genetic population structure of the vulnerable bog fritillary butterfly.

Science.gov (United States)

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.

Structural parameters of pikeperch (Sander lucioperca population of the Kyiv reservoir

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O. Buzevych

2017-01-01

Full Text Available Purpose. Analysis of the dynamics of structural parameters as an integral property of the processes of recruitment and elimination of the reproductive and commercial population nuclei of pikeperch of the Kyiv reservoir. Methodology. Ichthyological material was collected during spring-summer period of 2015-2016 from survey catches done with gill nets with mesh sizes of 30-120 mm. Collection and processing of the field materials were carried out using conventional methods. In total, catches of 3.5 thousand net-days were processed during the study period and 1031 individual pikeperch were analyzed. Total mortality coefficient (Z was determined by graphic method based on the dynamics of the natural logarithms of the abundances of different age groups. Statistical processing of data was done in MS Excel. Findings. Commercial landings of pikeperch during last 10 years has a clear trend for a growth: from 20-25 to 80-100 tons. The catch of pikeperch per unit effort of survey gill nets in an interannual aspect is also characterized by a growth. At the same time, there is a certain improvement of the structural parameters of pikeperch population, e.g. an increase in the maximum age and extension of the modal frequency distribution. Age-3 and age-4 fish represented the major part of the population (71.6% in the catches of 2015, while the share of age-5-6 fish was also relatively high (10.8%. It resulted in an increase in the weighed mean age of the pikeperch population to 4.5 years. For 2016, there is a significant shift of the frequency distribution to its left wing – the major part of the population (64.7% was composed of age-2 to age-4 fish. The weighed mean age in 2016 decreased to 2.6 years that was due first of all to abundant recruitment and intensive elimination of middle age groups. Total mortality (Z of pikeperch in 2015-2016 was 0.53-0.56 that corresponded to normal conditions of the formation of the commercial stock of this species and

Stage-Structured Population Dynamics of AEDES AEGYPTI

Science.gov (United States)

Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations.

Science.gov (United States)

Garland, Ellen C; Goldizen, Anne W; Lilley, Matthew S; Rekdahl, Melinda L; Garrigue, Claire; Constantine, Rochelle; Hauser, Nan Daeschler; Poole, M Michael; Robbins, Jooke; Noad, Michael J

2015-08-01

For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of

Competition in size-structured populations: mechanisms inducing cohort formation and population cycles.

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de Roos, André M; Persson, Lennart

2003-02-01

In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and adults both feed on one and the same resource and hence interact by means of exploitative competition. Juvenile individuals allocate all assimilated energy into development and mature on reaching a fixed developmental threshold. The combination of this fixed threshold and the resource-dependent developmental rate, implies that the juvenile delay between birth and the onset of reproduction may vary in time. Adult individuals allocate all assimilated energy to reproduction. Mortality of both juveniles and adults is assumed to be inversely proportional to the amount of energy assimilated. In this setting we study how the dynamics of the population are influenced by the relative foraging capabilities of juveniles and adults. In line with results that we previously obtained in size-structured consumer-resource models with pulsed reproduction, population cycles primarily occur when either juveniles or adults have a distinct competitive advantage. When adults have a larger per capita feeding rate and are hence competitively superior to juveniles, population oscillations occur that are primarily induced by the fact that the duration of the juvenile period changes with changing food conditions. These cycles do not occur when the juvenile delay is a fixed parameter. When juveniles are competitively superior, two different types of population fluctuations can occur: (1) rapid, low-amplitude fluctuations having a period of half the juvenile delay and (2) slow, large-amplitude fluctuations characterized by a period, which is roughly equal to the juvenile delay. The analysis of simplified versions of the structured model indicates that these two types of oscillations also occur if

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

Science.gov (United States)

Rico, Y; Wagner, H H

2016-11-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Science.gov (United States)

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

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

OpenAIRE

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

2012-01-01

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 hierar...

Population and evolutionary dynamics in spatially structured seasonally varying environments.

Science.gov (United States)

Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

2018-03-25

Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

Genetic population structure of Shoal Bass within their native range

Science.gov (United States)

Taylor, Andrew T.; Tringali, Michael D.; Sammons, Steven M.; Ingram, Travis R.; O'Rouke, Patrick M.; Peterson, Douglas L.; Long, James M.

2018-01-01

Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites (N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is

Spatial and population genetic structure of microsatellites in white pine

Science.gov (United States)

Paula E. Marquardt; Bryan K. Epperson

2004-01-01

We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

Science.gov (United States)

Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

2011-04-05

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

A Structure for Population Education: Goals, Generalizations, and Behavioral Objectives.

Science.gov (United States)

Lane, Mary Turner; Wileman, Ralph E.

This book is written to assist anyone who wants to learn about, teach, or plan curricula for population education. A structure is provided that educators can use for first graders or for high school students. Chapter 1 identifies the population phenomenon and the need to study it. Chapter 2 gives the elements of the structure: goals,…

skeleSim: an extensible, general framework for population genetic simulation in R

Science.gov (United States)

Parobek, Christian M.; Archer, Frederick I.; DePrenger-Levin, Michelle E.; Hoban, Sean M.; Liggins, Libby; Strand, Allan E.

2016-01-01

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares’ complex capabilities, composing code and input files, a daunting bioinformatics barrier, and a steep conceptual learning curve. skeleSim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics, and organizing data output, in a reproducible pipeline within the R environment. skeleSim is designed to be an extensible framework that can ‘wrap’ around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skeleSim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skeleSim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skeleSim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). PMID:27736016

Population structure of larch forests in the Urals

Energy Technology Data Exchange (ETDEWEB)

Putenikhin, V.P.; Farukshina, G.G. [Russian Academy of Sciences, Ufa (Russian Federation). Botanical Garden Inst.

1995-12-31

The variability and population structure of larch (Larix sukaczewii Dyl.) naturally growing in the Urals was studied on the basis of biometric analysis of generative organs. The obtained results point to the existence of 11 phenotypically different local populations of Larix sukaczewii in the Urals. Four populations are identified in the South Urals: Marginal, central, high-mountainous, south-uralian and Bashkircis-uralian. Middle-uralian, Perm cis-uralian, central north-uralian and high-mountainous north-uralian populations are determined in the Middle and the North Urals. Three populations of Larix sukaczewii are identified in the Sub-Polar and the Polar Urals: Subpolar-uralian, Pechora-Thiman cisuralian and polar-uralian. 8 refs, 2 tabs

Population structure of larch forests in the Urals

Energy Technology Data Exchange (ETDEWEB)

Putenikhin, V P; Farukshina, G G [Russian Academy of Sciences, Ufa (Russian Federation). Botanical Garden Inst.

1996-12-31

The variability and population structure of larch (Larix sukaczewii Dyl.) naturally growing in the Urals was studied on the basis of biometric analysis of generative organs. The obtained results point to the existence of 11 phenotypically different local populations of Larix sukaczewii in the Urals. Four populations are identified in the South Urals: Marginal, central, high-mountainous, south-uralian and Bashkircis-uralian. Middle-uralian, Perm cis-uralian, central north-uralian and high-mountainous north-uralian populations are determined in the Middle and the North Urals. Three populations of Larix sukaczewii are identified in the Sub-Polar and the Polar Urals: Subpolar-uralian, Pechora-Thiman cisuralian and polar-uralian. 8 refs, 2 tabs

Genetic Diversity and Structure among Isolated Populations of the Endangered Gees Golden Langur in Assam, India

Science.gov (United States)

Biswas, Jihosuo; Nag, Sudipta; Shil, Joydeep; Umapathy, Govindhaswamy

2016-01-01

Gee’s golden langur (Trachypithecus geei) is an endangered colobine primate, endemic to the semi-evergreen and mixed-deciduous forests of Indo-Bhutan border. During the last few decades, extensive fragmentation has caused severe population decline and local extinction of golden langur from several fragments. However, no studies are available on the impact of habitat fragmentation and the genetic diversity of golden langur in the fragmented habitats. The present study aimed to estimate the genetic diversity in the Indian population of golden langur. We sequenced and analyzed around 500 bases of the mitochondrial DNA (mtDNA) hypervariable region-I from 59 fecal samples of wild langur collected from nine forest fragments. Overall, genetic diversity was high (h = 0.934, π = 0.0244) and comparable with other colobines. Populations in smaller fragments showed lower nucleotide diversity compared to the larger forest fragments. The median-joining network of haplotypes revealed a genetic structure that corresponded with the geographical distribution. The Aie and Champabati Rivers were found to be a barrier to gene flow between golden langur populations. In addition, it also established that T. geei is monophyletic but revealed possible hybridization with capped langur, T. pileatus, in the wild. It is hoped that these findings would result in a more scientific approach towards managing the fragmented populations of this enigmatic species. PMID:27564405

Fine-scale population structure and the era of next-generation sequencing.

Science.gov (United States)

Henn, Brenna M; Gravel, Simon; Moreno-Estrada, Andres; Acevedo-Acevedo, Suehelay; Bustamante, Carlos D

2010-10-15

Fine-scale population structure characterizes most continents and is especially pronounced in non-cosmopolitan populations. Roughly half of the world's population remains non-cosmopolitan and even populations within cities often assort along ethnic and linguistic categories. Barriers to random mating can be ecologically extreme, such as the Sahara Desert, or cultural, such as the Indian caste system. In either case, subpopulations accumulate genetic differences if the barrier is maintained over multiple generations. Genome-wide polymorphism data, initially with only a few hundred autosomal microsatellites, have clearly established differences in allele frequency not only among continental regions, but also within continents and within countries. We review recent evidence from the analysis of genome-wide polymorphism data for genetic boundaries delineating human population structure and the main demographic and genomic processes shaping variation, and discuss the implications of population structure for the distribution and discovery of disease-causing genetic variants, in the light of the imminent availability of sequencing data for a multitude of diverse human genomes.

Global population structure of the spiny dogfish Squalus acanthias, a temperate shark with an antitropical distribution.

Science.gov (United States)

Veríssimo, A; McDowell, J R; Graves, J E

2010-04-01

The spiny dogfish (Squalus acanthias) is a temperate, coastal squaloid shark with an antitropical distribution in the Atlantic and Pacific oceans. The global population structure of this species is poorly understood, although individuals are known to undergo extensive migrations within coastal waters and across ocean basins. In this study, an analysis of the global population structure of the spiny dogfish was conducted using eight polymorphic nuclear microsatellite markers and a 566-bp fragment of the mitochondrial ND2 gene region. A low level of genetic divergence was found among collections from the Atlantic and South Pacific basins, whereas a high level of genetic divergence was found among Pacific Ocean collections. Two genetically distinct groups were recovered by both marker classes: one exclusive to North Pacific collections, and one including collections from the South Pacific and Atlantic locations. The strong genetic break across the equatorial Pacific coincides with major regional differences in the life-history characters of spiny dogfish, suggesting that spiny dogfish in areas on either side of the Pacific equator have been evolving independently for a considerable time. Phylogeographic analyses indicate that spiny dogfish populations had a Pacific origin, and that the North Atlantic was colonized as a result of a recent range expansion from the South American coast. Finally, the available data strongly argue for the taxonomic separation of the North Pacific spiny dogfish from S. acanthias and a re-evaluation of the specific status of S. acanthias is warranted.

Applications of Extensive Green-roof Systems in Contributing to Sustainable Development in Densely Populated Cities: a Hong Kong Study

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Xiaoling Zhang

2011-03-01

Full Text Available Developed cities such as Hong Kong are usually densely populated. Since the land is limited, high-rise buildings are constructed. When the building height becomes higher, air flow is reduced and heat is trapped among high-rise buildings. Air temperature will be greatly increased and air pollution becomes a serious problem. This creates a walled building problem. To reduce air temperature caused by the wall-effects, various methods have been developed in the previous studies. One typical method is the use of green roof systems. The application of extensive green roofs on the existing building rooftops has been recommended in Hong Kong since 2001. The advantage of this practice is that no additional floor area is required and it can also improve urban greenery. Although a green roof system has been introduced and adopted in Hong Kong since 2001, the emphasis is mainly given to the application of intensive green roofs for podium garden instead of extensive green roofs. It is considered valuable and necessary of the extensive green roofs for the buildings. This paper investigates the current practice of using extensive green roofs in Hong Kong. The constraints in applying extensive green roofs are investigated, which leads to studying the solutions for mitigating these constraints and improving the future development of the implementation.

Morphological Variation and Ecological Structure of Iroko (Milicia excelsa Welw. C.C. Berg) Populations across Different Bio geographical Zones in Benin

International Nuclear Information System (INIS)

Ouinsavi, C.; Sokpon, N.

2010-01-01

Iroko (Milicia excelsa) is a commercially important timber tree species formerly known by local people in Benin. Because of the highly attractive technological properties of its wood and its multipurpose uses, the species was subjected to intensive human pressure. Apart from strong climate oscillation during the Pleistocene, human caused habitat fragmentation through continuous land clearing for agriculture, extensive forests exploitation and urbanization induced the occurrence of many isolated forest plots and trees species among which Milicia excelsa trees. As fragmentation was proved to have deleterious effects on genetic diversity within a species and its morphological structure, it was of interest to investigate the current demographic, morphological and genetic structure of M. excelsa before coming up with conservation strategies. In the current study, morphological variation and ecological structure of M. excelsa populations were assessed in Benin using transect sampling method and multivariate analyses including principal component, cluster and canonical discriminant analyses. On the basis of morphological parameters, M. excelsa individuals and populations were clustered into four and discrimination of groups indicated that most of variations were highly related to edaphic factors and annual rainfall. Erratic diameter distribution was found for many populations although most of them showed bell shaped diameter distribution.

Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

Science.gov (United States)

Southwell, Colin; Emmerson, Louise; McKinlay, John; Newbery, Kym; Takahashi, Akinori; Kato, Akiko; Barbraud, Christophe; DeLord, Karine; Weimerskirch, Henri

2015-01-01

Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations.

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Colin Southwell

Full Text Available Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Science.gov (United States)

Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

2011-01-01

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia. PMID:21483678

Genetic diversity and population structure of leaf-nosed bat ...

African Journals Online (AJOL)

Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

Science.gov (United States)

Regidor-Cerrillo, Javier; Díez-Fuertes, Francisco; García-Culebras, Alicia; Moore, Dadín P.; González-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Díaz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

2013-01-01

The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal

Population structure and infectious disease risk in southern Africa.

Science.gov (United States)

Uren, Caitlin; Möller, Marlo; van Helden, Paul D; Henn, Brenna M; Hoal, Eileen G

2017-06-01

The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.

Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus.

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Masatoshi Matsunami

Full Text Available The Hokkaido salamander (Hynobius retardatus is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies.

Diversity and population structure of red rice germplasm in Bangladesh.

Science.gov (United States)

Islam, M Z; Khalequzzaman, M; Prince, M F R K; Siddique, M A; Rashid, E S M H; Ahmed, M S U; Pittendrigh, B R; Ali, M P

2018-01-01

While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.

Information Needs and Source Information of Agricultural Extension Workers in DIY

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Retno Wulandari

2016-02-01

Full Text Available One of the important factors that contribute to agricultural development is information. As such agricultural extension workers that link agricultural agencies to the farmers must have adequate and up-to-date information about agricultural practices before they could inform, educate and train the farmers in method and techniques of farming. This study aims to determine the types of information needed by agricultural extension workers; to determine the sources of information used by the agricultural extension workers; and to determine the comparison between types of information with information sources used by agricultural extension workers. The present study was a descriptive study using a survey design and conducted at Daerah Istimewa Yogyakarta (DIY Province. The populations of the study consists 181 agricultural extension workers divisible in the district level, namely Sleman, Kulon Progo, Gunung Kidul dan Bantul. Sampling procedure in this study used cluster sampling. The method for gathering data from the respondents is based on a structured questionnaire. Descriptive statistics was to describe the characteristics of the respondents and the dependent variables of the study. As a result, most of agricultural extension workers strongly needed the innovation information in seeking information followed by extension service information and extension role information. The result of information sources used by agricultural extension worker for extension service information, innovation information and extension role information indicates that agricultural extension workers used interpersonal source. Most of them never sought information use Internet, they use radio more frequently than television and video, agricultural extension worker also used mass media as information source.

Subring Depth, Frobenius Extensions, and Towers

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Lars Kadison

2012-01-01

Full Text Available The minimum depth d(B,A of a subring B⊆A introduced in the work of Boltje, Danz and Külshammer (2011 is studied and compared with the tower depth of a Frobenius extension. We show that d(B,A < ∞ if A is a finite-dimensional algebra and Be has finite representation type. Some conditions in terms of depth and QF property are given that ensure that the modular function of a Hopf algebra restricts to the modular function of a Hopf subalgebra. If A⊇B is a QF extension, minimum left and right even subring depths are shown to coincide. If A⊇B is a Frobenius extension with surjective Frobenius, homomorphism, its subring depth is shown to coincide with its tower depth. Formulas for the ring, module, Frobenius and Temperley-Lieb structures are noted for the tower over a Frobenius extension in its realization as tensor powers. A depth 3 QF extension is embedded in a depth 2 QF extension; in turn certain depth n extensions embed in depth 3 extensions if they are Frobenius extensions or other special ring extensions with ring structures on their relative Hochschild bar resolution groups.

Estimation of age structure of fish populations from length-frequency data

International Nuclear Information System (INIS)

Kumar, K.D.; Adams, S.M.

1977-01-01

A probability model is presented to determine the age structure of a fish population from length-frequency data. It is shown that when the age-length key is available, maximum-likelihood estimates of the age structure can be obtained. When the key is not available, approximate estimates of the age structure can be obtained. The model is used for determination of the age structure of populations of channel catfish and white crappie. Practical applications of the model to impact assessment are discussed

Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from Two Oahu (Hawaii) populations.

Science.gov (United States)

Wollenberg, M S; Ruby, E G

2009-01-01

We resolved the intraspecific diversity of Vibrio fischeri, the bioluminescent symbiont of the Hawaiian sepiolid squid Euprymna scolopes, at two previously unexplored morphological and geographical scales. These scales ranged from submillimeter regions within the host light organ to the several kilometers encompassing two host populations around Oahu. To facilitate this effort, we employed both novel and standard genetic and phenotypic assays of light-organ symbiont populations. A V. fischeri-specific fingerprinting method and five phenotypic assays were used to gauge the genetic richness of V. fischeri populations; these methods confirmed that the symbiont population present in each adult host's light organ is polyclonal. Upon statistical analysis of these genetic and phenotypic population data, we concluded that the characteristics of symbiotic populations were more similar within individual host populations than between the two distinct Oahu populations of E. scolopes, providing evidence that local geographic symbiont population structure exists. Finally, to better understand the genesis of symbiont diversity within host light organs, the process of symbiosis initiation in newly hatched juvenile squid was examined both experimentally and by mathematical modeling. We concluded that, after the juvenile hatches, only one or two cells of V. fischeri enter each of six internal epithelium-lined crypts present in the developing light organ. We hypothesize that the expansion of different, crypt-segregated, clonal populations creates the polyclonal adult light-organ population structure observed in this study. The stability of the luminous-bacterium-sepiolid squid mutualism in the presence of a polyclonal symbiont population structure is discussed in the context of contemporary evolutionary theory.

Evolutionary genomics and population structure of Entamoeba histolytica

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Koushik Das

2014-11-01

Full Text Available Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba.

Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

Science.gov (United States)

Yoon, M; Park, W; Nam, Y K; Kim, D S

2012-02-01

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

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Rocío Pineda-Martos

2014-01-01

Full Text Available Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms.

The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae) Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

Science.gov (United States)

Pineda-Martos, Rocío; Pujadas-Salvà, Antonio J.; Fernández-Martínez, José M.; Stoyanov, Kiril; Pérez-Vich, Begoña

2014-01-01

Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms. PMID:25143963

Population structure of Staphylococcus aureus in China

NARCIS (Netherlands)

Yan, Xiaomei

2015-01-01

The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance

Social structural consequences of population growth.

Science.gov (United States)

Adams, R E

1981-01-01

Estimates from archaeological data of the numbers in the elite classes, nonelite occupational specialists, density of population, city size, and size of political units in the ancient Maya civilization suggest that there was a quantum shift in rate of development in the Early Classic period, associated with intensification of agriculture, and that the social structure approximated to a generalized feudal pattern.

Patterns of admixture and population structure in native populations of Northwest North America.

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Paul Verdu

2014-08-01

Full Text Available The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

Perception of Extension Specialists about the Role of Extension in the Production and Adoption of the Genetically Modified Crops in Iran

OpenAIRE

Seyed J.F. Hosseini

2008-01-01

Extension specialists were surveyed in order to explore their perception about the role of extension in the production and adoption of Genetically Modified (GM) crops in Iran. The methodology used in this study involved a combination of descriptive and quantitative research. The total population for this study was 120 extension specialists in Iran. Extension specialists believed that the first priority of extension should be to increase the participation of stakeholders in the development of ...

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...

Age structure changes and extraordinary lifespan in wild medfly populations.

Science.gov (United States)

Carey, James R; Papadopoulos, Nikos T; Müller, Hans-Georg; Katsoyannos, Byron I; Kouloussis, Nikos A; Wang, Jane-Ling; Wachter, Kenneth; Yu, Wei; Liedo, Pablo

2008-06-01

The main purpose of this study was to test the hypotheses that major changes in age structure occur in wild populations of the Mediterranean fruit fly (medfly) and that a substantial fraction of individuals survive to middle age and beyond (> 3-4 weeks). We thus brought reference life tables and deconvolution models to bear on medfly mortality data gathered from a 3-year study of field-captured individuals that were monitored in the laboratory. The average time-to-death of captured females differed between sampling dates by 23.9, 22.7, and 37.0 days in the 2003, 2004, and 2005 field seasons, respectively. These shifts in average times-to-death provided evidence of changes in population age structure. Estimates indicated that middle-aged medflies (> 30 days) were common in the population. A surprise in the study was the extraordinary longevity observed in field-captured medflies. For example, 19 captured females but no reference females survived in the laboratory for 140 days or more, and 6 captured but no reference males survived in the laboratory for 170 days or more. This paper advances the study of aging in the wild by introducing a new method for estimating age structure in insect populations, demonstrating that major changes in age structure occur in field populations of insects, showing that middle-aged individuals are common in the wild, and revealing the extraordinary lifespans of wild-caught individuals due to their early life experience in the field.

Dynamics of a physiologically structured population in a time-varying environment

DEFF Research Database (Denmark)

Heilmann, Irene Louise Torpe; Starke, Jens; Andersen, Ken Haste

2016-01-01

Physiologically structured population models have become a valuable tool to model the dynamics of populations. In a stationary environment such models can exhibit equilibrium solutions as well as periodic solutions. However, for many organisms the environment is not stationary, but varies more...... or less regularly. In order to understand the interaction between an external environmental forcing and the internal dynamics in a population, we examine the response of a physiologically structured population model to a periodic variation in the food resource. We explore the addition of forcing in two...... cases: (A) where the population dynamics is in equilibrium in a stationary environment, and (B) where the population dynamics exhibits a periodic solution in a stationary environment. When forcing is applied in case A, the solutions are mainly periodic. In case B the forcing signal interacts...

Constructing stage-structured matrix population models from life tables: comparison of methods

Directory of Open Access Journals (Sweden)

Masami Fujiwara

2017-10-01

Full Text Available A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates of a population and can be used for calculating an asymptotic finite population growth rate (λ and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used

Genetic diversity of Morato's Digger Toad, Proceratophrys moratoi: spatial structure, gene flow, effective size and the need for differential management strategies of populations

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Mauricio P. Arruda

2017-06-01

Full Text Available Abstract The Morato's Digger Toad, Proceratophrys moratoi, is a critically endangered toad species with a marked population decline in southern Brazilian Cerrado. Despite this, new populations are being discovered, primarily in the northern part of the distribution range, which raises a number of questions with regard to the conservation status of the species. The present study analyzed the genetic diversity of the species based on microsatellite markers. Our findings permitted the identification of two distinct management units. We found profound genetic structuring between the southern populations, on the left margin of the Tietê River, and all other populations. A marked reduction was observed in the contemporary gene flow among the central populations that are most affected by anthropogenic impacts, such as extensive sugar cane plantations, which presumably decreases habitat connectivity. The results indicated reduced diversity in the southern populations which, combined with a smaller effective population size, may make these populations more susceptible to extinction. We recommend the reclassification of P. moratoi as vulnerable and the establishment of a special protection program for the southern populations. Our results provide important insights about the local extinction of southern populations of this toad.

A resolution to the blue whiting (Micromesistius poutassou) population paradox?

OpenAIRE

Pointin, Fabien; Payne, Mark R.

2014-01-01

We provide the strongest evidence to date supporting the existence of two independent blue whiting (Micromesistius poutassou (Risso, 1827)) populations in the North Atlantic. In spite of extensive data collected in conjunction with the fishery, the population structure of blue whiting is poorly understood. On one hand, genetic, morphometric, otolith and drift modelling studies point towards the existence of two populations, but, on the other hand, observations of adult distributions point tow...

Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

Science.gov (United States)

Zhan, Aibin; Li, Cheng; Fu, Jinzhong

2009-04-09

Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the

Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards

Science.gov (United States)

2013-01-01

Background Color traits in animals play crucial roles in thermoregulation, photoprotection, camouflage, and visual communication, and are amenable to objective quantification and modeling. However, the extensive variation in non-melanic pigments and structural colors in squamate reptiles has been largely disregarded. Here, we used an integrated approach to investigate the morphological basis and physical mechanisms generating variation in color traits in tropical day geckos of the genus Phelsuma. Results Combining histology, optics, mass spectrometry, and UV and Raman spectroscopy, we found that the extensive variation in color patterns within and among Phelsuma species is generated by complex interactions between, on the one hand, chromatophores containing yellow/red pteridine pigments and, on the other hand, iridophores producing structural color by constructive interference of light with guanine nanocrystals. More specifically, we show that 1) the hue of the vivid dorsolateral skin is modulated both by variation in geometry of structural, highly ordered narrowband reflectors, and by the presence of yellow pigments, and 2) that the reflectivity of the white belly and of dorsolateral pigmentary red marks, is increased by underlying structural disorganized broadband reflectors. Most importantly, these interactions require precise colocalization of yellow and red chromatophores with different types of iridophores, characterized by ordered and disordered nanocrystals, respectively. We validated these results through numerical simulations combining pigmentary components with a multilayer interferential optical model. Finally, we show that melanophores form dark lateral patterns but do not significantly contribute to variation in blue/green or red coloration, and that changes in the pH or redox state of pigments provide yet another source of color variation in squamates. Conclusions Precisely colocalized interacting pigmentary and structural elements generate extensive

Population structure of barley landrace populations and gene-flow with modern varieties.

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Elisa Bellucci

Full Text Available Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population. We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

Earthworm ecology affects the population structure of their Verminephrobacter symbionts

DEFF Research Database (Denmark)

Macedo Viana, Flavia Daniela; Jensen, Christopher Erik; Macey, Michael

2016-01-01

from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and E. fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils; for both types, three distinct populations were...... across host individuals from the same population. Thus, host ecology shapes the population structure of the Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms indicate that Verminephrobacter can be transferred bi-parentally or via leaky horizontal transmission in high...

Generation time, net reproductive rate, and growth in stage-age-structured populations

DEFF Research Database (Denmark)

Steiner, Uli; Tuljapurkar, Shripad; Coulson, Tim

2014-01-01

examples to show how reproductive timing Tc and level R0 are shaped by stage dynamics (individual trait changes), selection on the trait, and parent-offspring phenotypic correlation. We also show how population structure can affect dispersion in reproduction among ages and stages. These macroscopic...... to age-structured populations. Here we generalize this result to populations structured by stage and age by providing a new, unique measure of reproductive timing (Tc) that, along with net reproductive rate (R0), has a direct mathematical relationship to and approximates growth rate (r). We use simple...

High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

Science.gov (United States)

Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

2013-01-01

Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

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Jun Zhang

Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

Diversity and population structure of red rice germplasm in Bangladesh.

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M Z Islam

Full Text Available While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35. While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V, a similar SSR analysis yielded only three major groups (I, II, and III, and a model-based population structure analysis yielded four (A, B, C and D. Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA, as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207 among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular

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.

Population structure of Aggarwals of north India as revealed by molecular markers.

Science.gov (United States)

Gupta, Vipin; Khadgawat, Rajesh; Ng, Hon Keung Tony; Kumar, Satish; Rao, Vadlamudi Raghavendra; Sachdeva, Mohinder Pal

2010-12-01

Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

Trading Stages: Life Expectancies in Structured Populations

Science.gov (United States)

Tuljapurkar, Shripad; Coulson, Tim; Horvitz, Carol

2012-01-01

Interest in stage-and age structured models has recently increased because they can describe quantitative traits such as size that are left out of age-only demography. Available methods for the analysis of effects of vital rates on lifespan in stage-structured models have not been widely applied because they are hard to use and interpret, and tools for age and stage structured populations are missing. We present easily interpretable expressions for the sensitivities and elasticities of life expectancy to vital rates in age-stage models, and illustrate their application with two biological examples. Much of our approach relies on trading of time and mortality risk in one stage for time and risk in others. Our approach contributes to the new framework of the study of age- and stage-structured biodemography. PMID:22664576

Genetic diversity and population structure of endangered Aquilaria ...

Indian Academy of Sciences (India)

2015-12-03

Dec 3, 2015 ... ... Aromatic and Economic Plants, CSIR - North-East Institute of Science and Technology ... and population structure is receiving tremendous attention for effective .... unreliable detection and to increase the quality of data. The.

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.

Population structure and genomic inbreeding in nine Swiss dairy cattle populations.

Science.gov (United States)

Signer-Hasler, Heidi; Burren, Alexander; Neuditschko, Markus; Frischknecht, Mirjam; Garrick, Dorian; Stricker, Christian; Gredler, Birgit; Bapst, Beat; Flury, Christine

2017-11-07

Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH ) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH : 0.027), OB (F ROH : 0.029), and SI (F ROH : 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH : 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service

Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border.

Science.gov (United States)

Larrañaga, Nerea; Mejía, Rosa E; Hormaza, José I; Montoya, Alberto; Soto, Aida; Fontecha, Gustavo A

2013-10-04

The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (H(e)) results were similarly low for both populations. A moderate differentiation was revealed by the F(ST) index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America.

Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

Science.gov (United States)

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

Genetic structure of Bemisia tabaci Med populations from home-range countries, inferred by nuclear and cytoplasmic markers : impact on the distribution of the insecticide resistance genes

OpenAIRE

Gauthier, Nathalie; Clouet, C.; Perrakis, A.; Kapantaidaki, D.; Peterschmitt, M.; Tsagkarakou, A.

2014-01-01

BACKGROUND: Insecticide resistance management in Bemisia tabaci is one of the main issues facing agricultural production today. An extensive survey was undertaken in five Mediterranean countries to examine the resistance status of Med B. tabaci species in its range of geographic origin and the relationship between population genetic structure and the distribution of resistance genes. The investigation combined molecular diagnostic tests, sequence and microsatellite polymorphism studies and mo...

Quantitative and Qualitative Extensions of Event Structures

NARCIS (Netherlands)

Katoen, Joost P.

1996-01-01

An important application of formal methods is the specification, design, and analysis of functional aspects of (distributed) systems. Recently the study of quantitative aspects of such systems based on formal methods has come into focus. Several extensions of formal methods where the occurrence of

Genetic structure of West Greenland populations of lumpfish Cyclopterus lumpus

DEFF Research Database (Denmark)

Mayoral, Elsa Garcia; Olsen, M.; Hedeholm, R.

2016-01-01

In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identifica...

Chronic irradiation as an ecological factor affecting genetic population structure

International Nuclear Information System (INIS)

Kal'chenko, V.A.; Kalabushkin, B.A.; Rubanovich, A.V.

1991-01-01

Genetic structure of two Centaurea scabiosa L. populations was studied by frequency distribution of leucine aminopeptidase (LAP) locus genotypes. The experimental population has been growing under conditions of chronic irradiation, with the dose per generation amounting to 1.2 to 25.5 Gy. In it, mutational variants are observed with a frequency of 5.4.10(-3)-4.5.10(-2) per generation (as compared to control population frequency at 5.4.10(-4)). Indexes for heterozygosity, mean number of genotypes, and effective number of alleles were higher in the experimental population. Segregation analysis revealed no differences in viability in the control population, and all genotypic combinations were found to be nearly neutral. In the experimental population, however, significant differences in relative viability of the genotypes were disclosed. The relative viability of heterozygotes for mutant allele C' was nearly maximum, while heterozygotes for other mutant alleles showed minimum viability. We reach the conclusion that the differences in genetic structure of the populations under investigation can be explained by the chronic irradiation factor that brought out differences in adaptability of both normal and mutant genotypes. The suggestion is that intra-locus interactions of the C' allele with normal alleles determine plant resistance to a wide range of unfavorable environmental conditions

Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers.

Science.gov (United States)

Filippi, Carla V; Aguirre, Natalia; Rivas, Juan G; Zubrzycki, Jeremias; Puebla, Andrea; Cordes, Diego; Moreno, Maria V; Fusari, Corina M; Alvarez, Daniel; Heinz, Ruth A; Hopp, Horacio E; Paniego, Norma B; Lia, Veronica V

2015-02-13

Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent

Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations

OpenAIRE

Garland, E.C.; Goldizen, A.W.; Lilley, M.S.; Rekdahl, M.L.; Garrigue, Claire; Constantine, R.; Hauser, N.D.; Poole, M.M.; Robbins, J.; Noad, M.J.

2015-01-01

For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of inf...

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

Science.gov (United States)

Gordon, Sean P; Contreras-Moreira, Bruno; Woods, Daniel P; Des Marais, David L; Burgess, Diane; Shu, Shengqiang; Stritt, Christoph; Roulin, Anne C; Schackwitz, Wendy; Tyler, Ludmila; Martin, Joel; Lipzen, Anna; Dochy, Niklas; Phillips, Jeremy; Barry, Kerrie; Geuten, Koen; Budak, Hikmet; Juenger, Thomas E; Amasino, Richard; Caicedo, Ana L; Goodstein, David; Davidson, Patrick; Mur, Luis A J; Figueroa, Melania; Freeling, Michael; Catalan, Pilar; Vogel, John P

2017-12-19

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

The impact of natural transformation on adaptation in spatially structured bacterial populations.

Science.gov (United States)

Moradigaravand, Danesh; Engelstädter, Jan

2014-06-20

Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida.

Science.gov (United States)

Fedrizzi, Nathan; Stiassny, Melanie L J; Boehm, J T; Dougherty, Eric R; Amato, George; Mendez, Martin

2015-01-01

The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as indicated by significant fixation indices. Despite an overall significant population structure, we observed evidence of interbreeding between individuals from geographically distant sites, supporting the hypothesis that rafting serves to maintain a degree of population connectivity. All individuals collected from Pensacola belong to a single distinct subpopulation, which is highly differentiated from the rest of Floridian dwarf seahorses sampled. Our findings highlight the utility of mtDNA markers in evaluating barriers to gene flow and identifying genetically distinct populations, which are vital to the development of comprehensive conservation strategies for exploited taxa.

Dynamique de structuration spatio-temporelle des populations de ...

African Journals Online (AJOL)

Dynamique de structuration spatio-temporelle des populations de familles de macroinvertébrés dans un continuum lac de barrage-effluent-fleuve issu de périmètre irrigué. Bassin de la Volta (Burkina Faso)

Structured populations with distributed recruitment : from PDE to delay formulation

NARCIS (Netherlands)

Calsina, Àngel; Diekmann, Odo; Farkas, József Z.

2016-01-01

In this work, first, we consider a physiologically structured population model with a distributed recruitment process. That is, our model allows newly recruited individuals to enter the population at all possible individual states, in principle. The model can be naturally formulated as a first-order

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing.

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Donatien F Chedom

2015-11-01

Full Text Available RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We would like to identify the underlying evolutionary structures. We utilize two sources of information to attempt this; within segment linkage information, and mutation prevalence. We demonstrate that clone haplotypes, their prevalence, and maximum parsimony reticulate evolutionary structures can be identified, although the solutions may not be unique, even for complete sets of information. This is applied to a chain of influenza infection, where we infer evolutionary structures, including reassortment, and demonstrate some of the difficulties of interpretation that arise from deep sequencing due to artifacts such as template switching during PCR amplification.

Sus scrofa: Population Structure, Reproduction and Condition in Tropical North Eastern Australia

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NELSON, John E.

2009-01-01

Full Text Available Three feral pig populations inhabiting contrasting environments along the north easterncoast of Australia have been investigated with respect to population structure, individual condition andreproduction. The population on Prince of Wales Island contains a large proportion of juvenile andsub-adult pigs but lacks pigs in the higher age classes. Individuals also breed at an earlier age thananimals of the mainland populations. Pig populations on Cape York Peninsula show a largerproportion of older animals and feral pigs living in rainforest habitats show a low proportion ofanimals in very young and very old age classes. Pigs from the lowland rainforest population are inbetter condition than those of the other populations for most of the year, reflecting the availability offood all year round in this environment. Differences in the population structure of the threepopulations are discussed with respect to fecundity and several mortality factors such as predation anddiseases/parasites.

The Application of Contagious Disease Epidemiological Models to Known Population Structure and Movement

Science.gov (United States)

2016-03-01

concept model ( Ebola ) • Time-varying disease transmission rate () Influenza model • Population structure represented via finite scale-free network...I N S T I T U T E F O R D E F E N S E A N A L Y S E S The Application of Contagious Disease Epidemiological Models to Known Population Structure ...Known Population Structure and Movement Julia K. Burr Robert L. Cubeta Lucas A. LaViolet Carl A. Curling This page is intentionally blank. iii

Population estimates of extended family structure and size.

Science.gov (United States)

Garceau, Anne; Wideroff, Louise; McNeel, Timothy; Dunn, Marsha; Graubard, Barry I

2008-01-01

Population-based estimates of biological family size can be useful for planning genetic studies, assessing how distributions of relatives affect disease associations with family history and estimating prevalence of potential family support. Mean family size per person is estimated from a population-based telephone survey (n = 1,019). After multivariate adjustment for demographic variables, older and non-White respondents reported greater mean numbers of total, first- and second-degree relatives. Females reported more total and first-degree relatives, while less educated respondents reported more second-degree relatives. Demographic differences in family size have implications for genetic research. Therefore, periodic collection of family structure data in representative populations would be useful. Copyright 2008 S. Karger AG, Basel.

Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

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Federica Costantini

Full Text Available While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

Landscape structure mediates the effects of a stressor on field vole populations

DEFF Research Database (Denmark)

Dalkvist, Trine; Sibly, Richard M.; Topping, Christopher John

2013-01-01

Spatio-temporal landscape heterogeneity has rarely been considered in population-level impact assessments. Here we test whether landscape heterogeneity is important by examining the case of a pesticide applied seasonally to orchards which may affect non-target vole populations, using a validated ...... results show that accurate prediction of population impact cannot be achieved without taking account of landscape structure. The specifics of landscape structure and habitat connectivity are likely always important in mediating the effects of stressors....

Population genetic structure and demographic history of small ...

African Journals Online (AJOL)

Population genetic structure and demographic history of small yellow croaker, ... diversity (0.0112 ± 0.0061 to 0.0141 ± 0.0075) were detected in the species. ... into two closely related clades, but did not appear to have any geographic ...

Population structure of Tor tor inferred from mitochondrial gene cytochrome b.

Science.gov (United States)

Pasi, Komal Shyamakant; Lakra, W S; Bhatt, J P; Goswami, M; Malakar, A Kr

2013-06-01

Tor tor, commonly called as Tor mahseer, is a high-valued food and game fish endemic to trans-Himalayan region. Mitochondrial cytochrome b (cyt b) gene region of 967 bp was used to estimate the population structure of T. tor. Three populations of T. tor were collected from Narmada (Hosangabad), Ken (Madla), and Parbati river (Sheopur) in Madhya Pradesh, India. The sequence analysis revealed that the nucleotide diversity (π) was low, ranging from 0.000 to 0.0150. Haplotype diversity (h) ranged from 0.000 to 1.000. The analysis of molecular variance analysis indicated significant genetic divergence among the three populations of T. tor. Neighboring-joining tree also showed that all individuals from three populations clustered into three distinct clades. The data generated by cyt b marker revealed interesting insight about population structure of T. tor, which would serve as baseline data for conservation and management of mahseer fishery.

Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

Science.gov (United States)

Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

2015-08-01

Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

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

Science.gov (United States)

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

An age structured model for obesity prevalence dynamics in populations

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Gilberto González Parra

2010-08-01

Full Text Available Objective. Modeling the correlation of the development of obesity in a population with age and time and predict the dynamics of the correlation of the development of obesity in a population with age and time under different scenarios in Valencia (Spain. Materials and methods. An age structured mathematical model is used to describe the future dynamics of obesity prevalence for different ages in human population with excess weight. Simulation of the model with parameters estimated using the Health Survey of the Region of Valencia 2000 (4.319 interviews and Health Survey of the Region of Valencia 2005 (4.012 interviews. The model considers only overweight and obese populations since these subpopulations are the most relevant on obesity health concern. Results. The model allows predicting and studying the prevalence of obesity for each age. Results showed an increasing trend of obesity in the following years in well accordance with the trend observed in several countries. Conclusions. Based on the numerical simulations it is possible to conclude that the age structured mathematical model is suitable to forecast the obesity epidemic in each age group in different countries. Additionally, this type of models may be applied to study other characteristics of other populations such animal populations.

Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China.

Science.gov (United States)

Yi, Shaokui; Li, Yanhe; Shi, Linlin; Zhang, Long; Li, Qingbin; Chen, Jing

2018-04-03

The red swamp crayfish (Procambarus clarkii) is one of the most economically important farmed aquatic species in China. However, it is also a famous invasive species in the world. This invasive species was dispersed most via human activities including intentional or unintentional carry in China. Thus, P. clarkii naturally distributed in China provides us a desirable mode to investigate the genetic structure of an invasive species dispersed mainly by human-mediated factors. To reveal the impact of human-mediated dispersal on genetic structure of P. clarkii in China, a total of 22,043 genome-wide SNPs were obtained from approximately 7.4 billion raw reads using 2b-RAD technique in this study. An evident pattern of population genetic structure and the asymmetrical migrational rates between different regions were observed with 22 populations based on these SNPs. This study provide a better understanding of the population genetic structure and demographic history of P. clarkii populations in China, inferring that anthropogenic factors (aquaculture or by accident) and ecological factors (e.g., complicated topography and climatic environment), as well as its special biological traits could account for the current population structure pattern and dispersal history of P. clarkii.

Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations.

Science.gov (United States)

Ben Halim, Nizar; Hsouna, Sana; Lasram, Khaled; Chargui, Mariem; Khemira, Laaroussi; Saidane, Rachid; Abdelhak, Sonia; Kefi, Rym

2018-02-01

Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (n = 4857) were compiled from previous studies. The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.

Producing genome structure populations with the dynamic and automated PGS software.

Science.gov (United States)

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

2018-05-01

Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

Estimating spatio-temporal dynamics of size-structured populations

DEFF Research Database (Denmark)

Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

2014-01-01

with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

Modeling livestock population structure: a geospatial database for Ontario swine farms.

Science.gov (United States)

Khan, Salah Uddin; O'Sullivan, Terri L; Poljak, Zvonimir; Alsop, Janet; Greer, Amy L

2018-01-30

Infectious diseases in farmed animals have economic, social, and health consequences. Foreign animal diseases (FAD) of swine are of significant concern. Mathematical and simulation models are often used to simulate FAD outbreaks and best practices for control. However, simulation outcomes are sensitive to the population structure used. Within Canada, access to individual swine farm population data with which to parameterize models is a challenge because of privacy concerns. Our objective was to develop a methodology to model the farmed swine population in Ontario, Canada that could represent the existing population structure and improve the efficacy of simulation models. We developed a swine population model based on the factors such as facilities supporting farm infrastructure, land availability, zoning and local regulations, and natural geographic barriers that could affect swine farming in Ontario. Assigned farm locations were equal to the swine farm density described in the 2011 Canadian Census of Agriculture. Farms were then randomly assigned to farm types proportional to the existing swine herd types. We compared the swine population models with a known database of swine farm locations in Ontario and found that the modeled population was representative of farm locations with a high accuracy (AUC: 0.91, Standard deviation: 0.02) suggesting that our algorithm generated a reasonable approximation of farm locations in Ontario. In the absence of a readily accessible dataset providing details of the relative locations of swine farms in Ontario, development of a model livestock population that captures key characteristics of the true population structure while protecting privacy concerns is an important methodological advancement. This methodology will be useful for individuals interested in modeling the spread of pathogens between farms across a landscape and using these models to evaluate disease control strategies.

Consolidating birth-death and death-birth processes in structured populations.

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Joshua Zukewich

Full Text Available Network models extend evolutionary game theory to settings with spatial or social structure and have provided key insights on the mechanisms underlying the evolution of cooperation. However, network models have also proven sensitive to seemingly small details of the model architecture. Here we investigate two popular biologically motivated models of evolution in finite populations: Death-Birth (DB and Birth-Death (BD processes. In both cases reproduction is proportional to fitness and death is random; the only difference is the order of the two events at each time step. Although superficially similar, under DB cooperation may be favoured in structured populations, while under BD it never is. This is especially troubling as natural populations do not follow a strict one birth then one death regimen (or vice versa; such constraints are introduced to make models more tractable. Whether structure can promote the evolution of cooperation should not hinge on a simplifying assumption. Here, we propose a mixed rule where in each time step DB is used with probability δ and BD is used with probability 1-δ. We derive the conditions for selection favouring cooperation under the mixed rule for all social dilemmas. We find that the only qualitatively different outcome occurs when using just BD (δ = 0. This case admits a natural interpretation in terms of kin competition counterbalancing the effect of kin selection. Finally we show that, for any mixed BD-DB update and under weak selection, cooperation is never inhibited by population structure for any social dilemma, including the Snowdrift Game.

Population structure of Nellore cattle in northeastern Brazil

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Ana Carla Borges Barbosa

2013-09-01

Full Text Available The objective of this study was to evaluate the population genetic structure of Nellore cattle in northeastern Brazil. Pedigree information was collected from 175,231 animals born from 1967 to 2007. Probability of gene origin, inbreeding, average relatedness coefficient (AR, completeness pedigree, effective population size and generation interval were calculated. Generation interval was high due to the long period of time animals were used as reproducers. The bottleneck effect was evidenced as a result of intensive use of limited breeders over the last years. Low values were observed ​​in the effective number of founder animals (434 and ancestors (427 comparing with the number on the base (175,231 and reference populations (130,038. Generally, the variability explained by the founders and ancestors is considered low. The average coefficient of inbreeding (0.11% and AR (0.14% estimated for this population is considered low and can be partly explained by the increased population effective number in recent periods; however, it may be underestimated by shallow pedigree.

Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

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Silvia Matesanz

Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

Big mountains but small barriers: Population genetic structure of the Chinese wood frog (Rana chensinensis in the Tsinling and Daba Mountain region of northern China

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Li Cheng

2009-04-01

Full Text Available Abstract Background Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Results Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. Conclusion The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high

Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides)

Science.gov (United States)

Colin M. Callahan; Carol A. Rowe; Ronald J. Ryel; John D. Shaw; Michael D. Madritch; Karen E. Mock

2013-01-01

Aspen populations in the south-western portion of the range are consistent with expectations for a historically stable edge, with low within-population diversity, significant geographical population structuring, and little evidence of northward expansion. Structuring within the southwestern cluster may result from distinct gene pools separated during the Pleistocene...

Population structure of fishes from an urban stream

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Naiara Zanatta

2017-05-01

Full Text Available The aim of this study was to identify the population structure of the ichthyofauna in an urban stream within an environmental protection area in southern Brazil. Quarterly samplings were conducted between October 2009 and August 2010. Poecilia reticulata was the most abundant species, followed by Hypostomus ancistroides and Rhamdia quelen. It was found a higher proportion of adults instead of juveniles from P. reticulata and R. quelen populations, while the opposite was recorded for H. ancistroides. Sex ratio of 1:1 was found for H. ancistroides, but differed significantly for P. reticulata and R. quelen. Females of P. reticulata and R. quelen reached higher length than males in the smaller and higher length-classes, while H. ancistroides females were only longer in initial length-classes. It was recorded higher occurrence of mature and maturing individuals. Mature individuals of H. ancistroides were sampled in October, and P. reticulata and R. quelen throughout the sampling period. Despite adverse environmental conditions, the occurrence of juveniles indicates reproductive activity for these species. Population structure studies in degraded systems are urgent, since life-history features of species may suffer changes due to anthropic impacts. Providing such information contributes to decision making and management of degraded systems.

Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

Science.gov (United States)

Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

2011-01-01

Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

Population structure of giraffes is affected by management in the Great Rift Valley, Kenya.

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Zoe Muller

Full Text Available Giraffe populations in East Africa have declined in the past thirty years yet there has been limited research on this species. This study had four objectives: i to provide a baseline population assessment for the two largest populations of Rothschild's giraffes in Kenya, ii to assess whether there are differences in population structure between the two enclosed populations, iii to assess the potential and possible implications of different management practices on enclosed giraffe populations to inform future decision-making, and iv to add to the availability of information available about giraffes in the wild. I used individual identification to assess the size and structure of the two populations; in Soysambu Conservancy between May 2010 and January 2011, I identified 77 giraffes; in Lake Nakuru National Park between May 2011 and January 2012, I identified 89. Population structure differed significantly between the two sites; Soysambu Conservancy contained a high percentage of juveniles (34% and subadults (29% compared to Lake Nakuru NP, which contained fewer juveniles (5% and subadults (15%. During the time of this study Soysambu Conservancy contained no lions while Lake Nakuru NP contained a high density of lions (30 lions per 100km2. Lions are the main predator of giraffes, and preferential predation on juvenile giraffes has previously been identified in Lake Nakuru NP. My results suggest that high lion density in Lake Nakuru NP may have influenced the structure of the giraffe population by removing juveniles and, consequently, may affect future population growth. I suggest that wildlife managers consider lion densities alongside breeding plans for Endangered species, since the presence of lions appears to influence the population structure of giraffes in enclosed habitats.

Population structure of giraffes is affected by management in the Great Rift Valley, Kenya.

Science.gov (United States)

Muller, Zoe

2018-01-01

Giraffe populations in East Africa have declined in the past thirty years yet there has been limited research on this species. This study had four objectives: i) to provide a baseline population assessment for the two largest populations of Rothschild's giraffes in Kenya, ii) to assess whether there are differences in population structure between the two enclosed populations, iii) to assess the potential and possible implications of different management practices on enclosed giraffe populations to inform future decision-making, and iv) to add to the availability of information available about giraffes in the wild. I used individual identification to assess the size and structure of the two populations; in Soysambu Conservancy between May 2010 and January 2011, I identified 77 giraffes; in Lake Nakuru National Park between May 2011 and January 2012, I identified 89. Population structure differed significantly between the two sites; Soysambu Conservancy contained a high percentage of juveniles (34%) and subadults (29%) compared to Lake Nakuru NP, which contained fewer juveniles (5%) and subadults (15%). During the time of this study Soysambu Conservancy contained no lions while Lake Nakuru NP contained a high density of lions (30 lions per 100km2). Lions are the main predator of giraffes, and preferential predation on juvenile giraffes has previously been identified in Lake Nakuru NP. My results suggest that high lion density in Lake Nakuru NP may have influenced the structure of the giraffe population by removing juveniles and, consequently, may affect future population growth. I suggest that wildlife managers consider lion densities alongside breeding plans for Endangered species, since the presence of lions appears to influence the population structure of giraffes in enclosed habitats.

Population structure, fluctuating asymmetry and genetic variability in an endemic and highly isolated Astyanax fish population (Characidae

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Maria Claudia Gross

2004-01-01

Full Text Available Morphological and chromosomal markers were used to infer the structure and genetic variability of a population of fish of the genus Astyanax, geographically isolated at sinkhole 2 of Vila Velha State Park, Paraná, Brazil. Two morphotypes types were observed, the standard phenotype I and phenotype II which showed an anatomical alteration probably due to an inbreeding process. Fluctuating asymmetry (FA analysis of different characters showed low levels of morphological variation among the population from sinkhole 2 and in another population from the Tibagi river (Paraná, Brazil. The Astyanax karyotype was characterized in terms of chromosomal morphology, constitutive heterochromatin and nucleolar organizer regions. Males and females presented similar karyotypes (2n=48, 6M+18SM+14ST+10A with no evidence of a sex chromosome system. One female from sinkhole 2 was a natural triploid with 2n=3x=72 chromosomes (9M+27SM+21ST+15A. The data are discussed regarding the maintenance of population structure and their evolutionary importance, our data suggesting that Astyanax from the Vila Velha State Park sinkhole 2 is a recently isolated population.

Weak and or non-existent farmer-research-extension linkage ...

African Journals Online (AJOL)

extension-farmer linkages in Nyanga district of Zimbabwe. The target sample population was comprised of 150 communal farmers (N=150) from three clusters in Nyanga districts, as well as 12 extension officers (N=12) and six research officers ...

Extensive reduction of surface UV radiation since 1750 in world's populated regions

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M. M. Kvalevåg

2009-10-01

Full Text Available Human activity influences a wide range of components that affect the surface UV radiation levels, among them ozone at high latitudes. We calculate the effect of human-induced changes in the surface erythemally weighted ultra-violet radiation (UV-E since 1750. We compare results from a radiative transfer model to surface UV-E radiation for year 2000 derived by satellite observations (from Total Ozone Mapping Spectroradiometer and to ground based measurements at 14 sites. The model correlates well with the observations; the correlation coefficients are 0.97 and 0.98 for satellite and ground based measurements, respectively. In addition to the effect of changes in ozone, we also investigate the effect of changes in SO₂, NO₂, the direct and indirect effects of aerosols, albedo changes and aviation-induced contrails and cirrus. The results show an increase of surface UV-E in polar regions, most strongly in the Southern Hemisphere. Furthermore, our study also shows an extensive surface UV-E reduction over most land areas; a reduction up to 20% since 1750 is found in some industrialized regions. This reduction in UV-E over the industrial period is particularly large in highly populated regions.

Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina

Science.gov (United States)

McCartney-Melstad, Evan; Waller, Tomás; Micucci, Patricio A.; Barros, Mariano; Draque, Juan; Amato, George; Mendez, Martin

2012-01-01

Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found in wetland systems in South America. These snakes are commercially harvested under a sustainable management plan in Argentina, so information regarding population structuring can be helpful for determination of management units. We evaluated genetic structure and migration using partial sequences from the mitochondrial control region and mitochondrial genes cyt-b and ND4 for 183 samples collected within northern Argentina. A group of landscape features and environmental variables including several treatments of temperature and precipitation were explored as potential drivers of observed genetic patterns. We found significant population structure between most putative population comparisons and bidirectional but asymmetric migration in several cases. The configuration of rivers and wetlands was found to be significantly associated with yellow anaconda population structure (IBD), and important for gene flow, although genetic distances were not significantly correlated with the environmental variables used here. More in-depth analyses of environmental data may be needed to fully understand the importance of environmental conditions on population structure and migration. These analyses indicate that our putative populations are demographically distinct and should be treated as such in Argentina's management plan for the harvesting of yellow anacondas. PMID:22675425

Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

Science.gov (United States)

Vickruck, J L; Richards, M H

2017-05-01

While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

Lack of Population Structure in Coriander Populations Based on SDS (Seed Storage Protein Page Analysis

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Gülsüm Yaldiz

2016-08-01

Full Text Available Genetic variation is prerequisite for plant breeding. Nothing information existed in the literature for available diversity of Coriander accession in Turkey. Plant breeding activities are negligible in Turkey. So in order to start effective plant breeding program in Turkey, information on the available genetic diversity is viable. Therefore we planned to study the genetic variation and population structure of 29 Coriander accessions by seed storage protein (SDS. SDS analysis elaborated the lack of population structure and genetic bottleneck in the Coriander accessions in Turkey. Based on the results of this study, it was clear that sampling strategy was not appropriate and plant introduction should be made from different sources and diverse genotypes should be used as parents to initialize the effective Turkish Coriander breeding program.

Insular Celtic population structure and genomic footprints of migration.

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Ross P Byrne

2018-01-01

Full Text Available Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits.

Detailed genetic structure of European bitterling populations in Central Europe

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Veronika Bartáková

2015-11-01

Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

Analysis of genetic diversity and population structure in upland ...

Indian Academy of Sciences (India)

Mulugeta Seyoum

2018-06-09

Jun 9, 2018 ... diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions ...... conservation of cotton germplasm in China (English abstract). ... and Alishah O. 2011 Inter simple sequence repeats (ISSR).

Review: Genetic diversity and population structure of cotton ...

African Journals Online (AJOL)

Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

Genetic diversity, population structure and marker trait associations ...

Indian Academy of Sciences (India)

Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

Population genetic structure of coral reef species Plectorhinchus ...

African Journals Online (AJOL)

The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 individuals were collected from 12 coral reefs in Xisha, Zhongsha and Nansha archipelagos and 22 haplotypes were obtained.

Earliest evidence for the structure of Homo sapiens populations in Africa

Science.gov (United States)

Scerri, Eleanor M. L.; Drake, Nick A.; Jennings, Richard; Groucutt, Huw S.

2014-10-01

Understanding the structure and variation of Homo sapiens populations in Africa is critical for interpreting multiproxy evidence of their subsequent dispersals into Eurasia. However, there is no consensus on early H. sapiens demographic structure, or its effects on intra-African dispersals. Here, we show how a patchwork of ecological corridors and bottlenecks triggered a successive budding of populations across the Sahara. Using a temporally and spatially explicit palaeoenvironmental model, we found that the Sahara was not uniformly ameliorated between ∼130 and 75 thousand years ago (ka), as has been stated. Model integration with multivariate analyses of corresponding stone tools then revealed several spatially defined technological clusters which correlated with distinct palaeobiomes. Similarities between technological clusters were such that they decreased with distance except where connected by palaeohydrological networks. These results indicate that populations at the Eurasian gateway were strongly structured, which has implications for refining the demographic parameters of dispersals out of Africa.

Microsatellite genetic distances between oceanic populations of the humpback whale (Megaptera novaeangliae)

NARCIS (Netherlands)

Valsecchi, E; Palsboll, P; Hale, P; GlocknerFerrari, D; Ferrari, M; Clapham, P; Larsen, F; Mattila, D; Sears, R; Sigurjonsson, J; Brown, M; Corkeron, P; Amos, B

Mitochondrial DNA haplotypes of humpback whales show strong segregation between oceanic populations and between feeding grounds within oceans, but this highly structured pattern does not exclude the possibility of extensive nuclear gene flow. Here we present allele frequency data for four

A Large Plasmodium vivax Reservoir and Little Population Structure in the South Pacific.

Directory of Open Access Journals (Sweden)

Cristian Koepfli

Full Text Available The importance of Plasmodium vivax in malaria elimination is increasingly being recognized, yet little is known about its population size and population genetic structure in the South Pacific, an area that is the focus of intensified malaria control.We have genotyped 13 microsatellite markers in 295 P. vivax isolates from four geographically distinct sites in Papua New Guinea (PNG and one site from Solomon Islands, representing different transmission intensities.Diversity was very high with expected heterozygosity values ranging from 0.62 to 0.98 for the different markers. Effective population size was high (12'872 to 19'533 per site. In PNG population structuring was limited with moderate levels of genetic differentiation. F ST values (adjusted for high diversity of markers were 0.14-0.15. Slightly higher levels were observed between PNG populations and Solomon Islands (F ST = 0.16.Low levels of population structure despite geographical barriers to transmission are in sharp contrast to results from regions of low P. vivax endemicity. Prior to intensification of malaria control programs in the study area, parasite diversity and effective population size remained high.

Gender inequality on the example of socio-demographic structures of Belgrade population

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Kuburović Ankica

2007-01-01

Full Text Available An analysis of demographic characteristics from the gender perspective represents a contribution to enlightening the social relations between female and male population in Belgrade. Gender specificity and explicitness of socio-demographic structures indicate to different positions and statuses of the female and male populations. There are more females than men in the total population of the capital city of Serbia. The sex imbalance of age groups is determined by gender differences in the number of born boys and girls, in migration characteristics and in the level of mortality. The male population is greater in the age group up to 20 years old, while the female population is more numerous among the middle-aged and older generations. Gender differences in marital structure, level of education and economic activities cannot be reduced only to demographic limits. A larger rate of married persons among the males in relation to female population is determined by the different behavior in view of remarriage in case of divorce or death of partner. Women are widowed or divorced more often than men, which can be interpreted as a less favorable position in everyday functioning, especially when the women have small or school-age children, as well as in the case of older women. Gender differences in the level of education of Belgrade population are not exceptionally pronounced and are a consequence of unfavorable positions of older women to a certain degree. Differences in economic activity, among other things, are determined by uneven utilization of female and male work force. The rate of economic activity is greater in the male population, and the coefficient of economic dependency in the female population. The gender difference in the rate of supported persons among the work capable population increases the unfavorable social position of women. The characteristics of socio-demographic structures of female and male population of the city of Belgrade vary

A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

DEFF Research Database (Denmark)

Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

2011-01-01

insight into consequences of population declines in a broader conservation context. The harbour seal population at Svalbard is the world's northernmost harbour seal population. Nothing is known about the genetic diversity, distinctiveness or origin of this small, marginalized mammalian population. Thus......  It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...

An analysis of the basic population structure of Shanghai Municipality.

Science.gov (United States)

Shen, A

1984-01-01

This paper analyzes the changes in Shanghai's population structure over the last 30 years in the 4 aspects of age structure, sex composition, urban and rural composition, and labor and employment structure. In 1953 those of the 0 to 6 age group accounted for 21.2% of the total population; in 1957 the group represented a proportion of 24.6%. Since the 1960s, especially after the 1970s, the family planning program gradually took effect, and the birthrate of the entire municipality fell drastically. The number of school-age children in 1979 was 1 1/2 times more than the same age group in 1953; there should be no worry that population control may result in a shortage of manpower to meet the needs of the work force and the armed forces either toward the end of this century or at the beginning of the next. The economy in China is underdeveloped, production and technology remain at a low level, average wages for employees are low, and for a long time the low living standard of the people has shown little sign of improvement. The problem is mainly manifest in the following areas: 1) distribution of the work force in heavy and light industries is not sufficiently rational, 2) the distribution of the work force between captial construction and transport and communications on the 1 hand and the national economy on the other is out of proportion, 3) the distribution of the work force between commerce, service trades, and public utilities on the 1 hand and the national economy on the other is disproportionated, and 4) the distribution of the work force between undertakings of culture, education, scientific research, health, and medical care on the 1 hand and economic construction on the other is improper. How to control population growth and adjust parts of the population structure to suit the national economic development poses a problem that calls for further in-depth study and analysis to resolve it step by step.

Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure.

Science.gov (United States)

Bohmann, Kristine; Gopalakrishnan, Shyam; Nielsen, Martin; Nielsen, Luisa Dos Santos Bay; Jones, Gareth; Streicker, Daniel G; Gilbert, M Thomas P

2018-04-19

Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large-scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large-scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure. © 2018 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

DEFF Research Database (Denmark)

Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

2014-01-01

The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

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

Directory of Open Access Journals (Sweden)

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.

Dynamic stress of impeller blade of shaft extension tubular pump device based on bidirectional fluid-structure interaction

Energy Technology Data Exchange (ETDEWEB)

Kan, Kan; Liu, Huiwen; Yang, Chunxia [Hohai University, Nanjing (China); Zheng, Yuan [National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Nanjing (China); Fu, Shifeng; Zhang, Xin [Power China Huadong Engineering Corporation, Hangzhou (China)

2017-04-15

Current research on the stability of tubular pumps is mainly concerned with the transient hydrodynamic characteristics. However, the structural response under the influence of fluid-structure interaction hasn't been taken fully into consideration. The instability of the structure can cause vibration and cracks, which may threaten the safety of the unit. We used bidirectional fluid-structure interaction to comprehensively analyze the dynamic stress characteristics of the impeller blades of the shaft extension tubular pump device. Furthermore, dynamic stress of impeller blade of shaft extension tubular pump device was solved under different lift conditions of 0° blade angle. Based on Reynolds-average N-S equation and SST k-ω turbulence model, numerical simulation was carried out for three-dimensional unsteady incompressible turbulent flow field of the pump device whole flow passage. Meanwhile, the finite element method was used to calculate dynamic characteristics of the blade structure. The blade dynamic stress distribution was obtained on the basis of fourth strength theory. The research results indicate that the maximum blade dynamic stress appears at the joint between root of inlet side of the blade suction surface and the axis. Considering the influence of gravity, the fluctuation of the blade dynamic stress increases initially and decreases afterwards within a rotation period. In the meantime, the dynamic stress in the middle part of inlet edge presents larger relative fluctuation amplitude. Finally, a prediction method for dynamic stress distribution of tubular pump considering fluid-structure interaction and gravity effect was proposed. This method can be used in the design stage of tubular pump to predict dynamic stress distribution of the structure under different operating conditions, improve the reliability of pump impeller and analyze the impeller fatigue life.

Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

Science.gov (United States)

Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

2016-06-17

In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

Genetic structure of typical and atypical populations of Candida albicans from Africa.

Science.gov (United States)

Forche, A; Schönian, G; Gräser, Y; Vilgalys, R; Mitchell, T G

1999-11-01

Atypical isolates of the pathogenic yeast Candida albicans have been reported with increasing frequency. To investigate the origin of a set of atypical isolates and their relationship to typical isolates, we employed a combination of molecular phylogenetic and population genetic analyses using rDNA sequencing, PCR fingerprinting, and analysis of co-dominant DNA nucleotide polymorphisms to characterize the population structure of one typical and two atypical populations of C. albicans from Angola and Madagascar. The extent of clonality and recombination was assessed in each population. The analyses revealed that the structure of all three populations of C. albicans was predominantly clonal but, as in previous studies, there was also evidence for recombination. Allele frequencies differed significantly between the typical and the atypical populations, suggesting very low levels of gene flow between them. However, allele frequencies were quite similar in the two atypical C. albicans populations, suggesting that they are closely related. Phylogenetic analysis of partial sequences encoding the nuclear 26S rDNA demonstrated that all three populations belong to a single monophyletic group, which includes the type strain of C. albicans. Copyright 1999 Academic Press.

76 FR 59113 - Extension of the Due Date for Submitting Information on How to Structure Proposed New Program...

Science.gov (United States)

2011-09-23

... manufacturing research needs, and issue sub-awards to fund research by universities, government laboratories, and U.S. businesses. This initiative would support research and development (R&D) in advanced...-02] Extension of the Due Date for Submitting Information on How to Structure Proposed New Program...

Population age structure and asset returns: an empirical investigation.

Science.gov (United States)

Poterba, J M

1998-10-01

"This paper investigates the association between population age structure, particularly the share of the population in the 'prime saving years' 45-60, and the returns on stocks and bonds. The paper is motivated by the claim that the aging of the 'Baby Boom' cohort in the United States is a key factor in explaining the recent rise in asset values. It also addresses the associated claim that asset prices will decline when this large cohort reaches retirement age and begins to reduce its asset holdings. This paper begins by considering household age-asset accumulation profiles. Data from the Survey of Consumer Finances suggest that while cross-sectional age-wealth profiles peak for households in their early 60s, cohort data on the asset ownership of the same households show a much less pronounced peak.... The paper then considers the historical relationship between demographic structure and real returns on Treasury bills, long-term government bonds, and corporate stock. The results do not suggest any robust relationship between demographic structure and asset returns.... The paper concludes by discussing factors such as international capital flows and forward-looking behavior on the part of market participants that could weaken the relationship between age structure and asset returns in a single nation." excerpt

Inter-chromosomal variation in the pattern of human population genetic structure

Directory of Open Access Journals (Sweden)

Baye Tesfaye M

2011-05-01

Full Text Available Abstract Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC, cluster, discriminant, fixation index (FST and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (OCA2, hect domain and RLD 2 (HERC2, ectodysplasin A receptor (EDAR and solute carrier family 45, member 2 (SLC45A2. These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (IFNG and death-associated protein kinase 1 (DAPK1, which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the

Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India.

Science.gov (United States)

Gaur, Uma; Tantia, Madhu Sudan; Mishra, Bina; Bharani Kumar, Settypalli Tirumala; Vijh, Ramesh Kumar; Chaudhury, Ashok

2018-03-01

The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise F ST value among populations was 0.4243 (p land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.

A Malthusian curb on spatial structure in microorganism populations.

Science.gov (United States)

Martin, A P

2004-10-07

That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

Science.gov (United States)

Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

2012-01-01

Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

Study of the matrimonial structure of the population of central Sardinia (Italy).

Science.gov (United States)

Vona, G; Francalacci, P; Paoli, G; Latini, V; Salis, M

1996-12-01

Temporal changes in the matrimonial structure of four Sardinian populations (Bitti, Lula, Lodè and Gavoi) have been studied. The endogamy rates and the average marriage distances indicate that the four villages experienced a long period of isolation. Only in recent decades endogamous marriages have fallen shortly. The trends of marital isonymy and inbreeding, evaluated both from isonymy and dispensation for consanguineous marriages, are similar to those of endogamy. The kinship values between pairs of populations show some preferential relationship (Bitti-Lodè, Lodè-Lula) and an evident differentiation between Gavoi and Bitti. The results also indicate that the values of kinship are not associated with the geographic distances. The possible impact of the matrimonial structure on the genetic structure and the relationships among the studied populations will be examined in further investigations, in which the genetic markers will be considered.

Genetic diversity and population structure of maize landraces from ...

African Journals Online (AJOL)

Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

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

Population structure of Staphylococcus aureus in China

OpenAIRE

Yan, Xiaomei

2015-01-01

The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance against rifampicin doubled to 68%. Staphylococcal food poisoning (SFP) is frequent in China. Two predominant S. aureus lineages, ST6 and ST943, were identified causing outbreaks of SFP in Southern China...

Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders

Directory of Open Access Journals (Sweden)

Rovito Sean M

2012-12-01

Full Text Available Abstract Background The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner. Results Deep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems. Conclusions Species of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B

Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.

Science.gov (United States)

Uren, Caitlin; Kim, Minju; Martin, Alicia R; Bobo, Dean; Gignoux, Christopher R; van Helden, Paul D; Möller, Marlo; Hoal, Eileen G; Henn, Brenna M

2016-09-01

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa. Copyright © 2016 by the Genetics Society of America.

Emotional decisions in structured populations for the evolution of public cooperation

Science.gov (United States)

Wang, Yongjie; Chen, Tong; Chen, Qiao; Si, Guangrun

2017-02-01

The behaviors of humans are not always profit-driven in public goods games (PGG). In addition, social preference and decision-making might be influenced, even changed by heuristics and conformity in the real life. Motivated by the facts, we would like to investigate the role of emotional system in cooperative behaviors of structured population in PGG. Meantime, the effects of diffusion of influence are studied in structured population. Numerical simulation results are indicated that emotions play very significant role indeed in emergence and maintenance of cooperation in structured populations in PGG. However, the influences of emotions on others are limited due to diminishing of influence diffusion and the existence of pure defectors. What is more, conformity, to some extent, could drive potentially more people to accept cooperative strategy with higher probability. Higher-level cooperation could be promoted as increasing values of synergy factors, but while the effects might diminish gradually as increasing number of positive heuristic players and conformist. Our work may be beneficial to address the social dilemmas in PGG.

Correlations in the population structure of music, genes and language

Science.gov (United States)

Brown, Steven; Savage, Patrick E.; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A.

2014-01-01

We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers. PMID:24225453

Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales

DEFF Research Database (Denmark)

Borrell, Asunción; Velásquez Vacca, Adriana; Pinela, Ana M.

2013-01-01

In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly......, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted....

Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population.

Science.gov (United States)

Gobena, Mesfin; Elzo, Mauricio A; Mateescu, Raluca G

2018-01-01

Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due

Population Structure and Genomic Breed Composition in an Angus–Brahman Crossbred Cattle Population

Directory of Open Access Journals (Sweden)

Mesfin Gobena

2018-03-01

Full Text Available Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus–Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus–Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage—indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals

Molecular epidemiology and population structure of bovine Streptococcus uberis

DEFF Research Database (Denmark)

Rato, M G; Bexiga, R; Nunes, S F

2008-01-01

The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations.

Science.gov (United States)

Wang, Yuchen; Lu, Dongsheng; Chung, Yeun-Jun; Xu, Shuhua

2018-01-01

Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied. We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant. These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization

KAUST Repository

Eriksson, Anders

2014-03-13

Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.

The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization

KAUST Repository

Eriksson, Anders; Manica, Andrea

2014-01-01

Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.

Population Genetic Structure of the People of Qatar

Science.gov (United States)

Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A.; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W.; Fuller, Jennifer; Hackett, Neil R.; Crystal, Ronald G.; Clark, Andrew G.

2010-01-01

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. PMID:20579625

Population genetic structure of the people of Qatar.

Science.gov (United States)

Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

2010-07-09

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Agricultural Extension. A Reference Manual.

Science.gov (United States)

Maunder, Addison, H.

The basic philosophy of agricultural extension was established in the more highly developed countries over the past century. Newly formed nations, the rural population of which formerly maintained a subsistence agriculture with limited industry, found it essential to establish a better-balanced economy. This led to a variety of rural services and…

Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity.

Science.gov (United States)

Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Piertney, Stuart B; Reid, Jane M

2017-09-01

A population's effective size (N e ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However, estimating N e , and identifying key demographic mechanisms that underlie the N e to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. A sophisticated demographic method of estimating N e /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated. However, this method requires detailed individual- and population-level data on sex- and age-specific reproduction and survival, and has rarely been implemented. Here, we use the reproductive value method and detailed demographic data to estimate N e /N for a small and apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population of high conservation concern. We additionally calculated two single-sample molecular genetic estimates of N e to corroborate the demographic estimate and examine evidence for unobserved immigration and gene flow. The demographic estimate of N e /N was 0.21, reflecting a high total demographic variance (σ2dg) of 0.71. Females and males made similar overall contributions to σ2dg. However, contributions varied among sex-age classes, with greater contributions from 3 year-old females than males, but greater contributions from ≥5 year-old males than females. The demographic estimate of N e was ~30, suggesting that rates of increase of inbreeding and loss of genetic variation per generation will be relatively high. Molecular genetic estimates of N e computed from linkage disequilibrium and approximate Bayesian computation were approximately 50 and 30, respectively, providing no evidence of substantial unobserved immigration which could bias demographic estimates of N e . Our analyses identify

Stochastic models for structured populations scaling limits and long time behavior

CERN Document Server

Meleard, Sylvie

2015-01-01

In this contribution, several probabilistic tools to study population dynamics are developed. The focus is on scaling limits of qualitatively different stochastic individual based models and the long time behavior of some classes of limiting processes. Structured population dynamics are modeled by measure-valued processes describing the individual behaviors and taking into account the demographic and mutational parameters, and possible interactions between individuals. Many quantitative parameters appear in these models and several relevant normalizations are considered, leading  to infinite-dimensional deterministic or stochastic large-population approximations. Biologically relevant questions are considered, such as extinction criteria, the effect of large birth events, the impact of  environmental catastrophes, the mutation-selection trade-off, recovery criteria in parasite infections, genealogical properties of a sample of individuals. These notes originated from a lecture series on Structured P...

Diversity and Genetic Variation among Brevipalpus Populations from Brazil and Mexico

Science.gov (United States)

Sánchez-Velázquez, E. J.; Santillán-Galicia, M. T.; Novelli, V. M.; Nunes, M. A.; Mora-Aguilera, G.; Valdez-Carrasco, J. M.; Otero-Colina, G.; Freitas-Astúa, J.

2015-01-01

Brevipalpus phoenicis s.l. is an economically important vector of the Citrus leprosis virus-C (CiLV-C), one of the most severe diseases attacking citrus orchards worldwide. Effective control strategies for this mite should be designed based on basic information including its population structure, and particularly the factors that influence its dynamics. We sampled sweet orange orchards extensively in eight locations in Brazil and 12 in Mexico. Population genetic structure and genetic variation between both countries, among locations and among sampling sites within locations were evaluated by analysing nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). In both countries, B. yothersi was the most common species and was found in almost all locations. Individuals from B. papayensis were found in two locations in Brazil. Brevipalpus yothersi populations collected in Brazil were more genetically diverse (14 haplotypes) than Mexican populations (four haplotypes). Although geographical origin had a low but significant effect (ca. 25%) on the population structure, the greatest effect was from the within location comparison (37.02 %). Potential factors driving our results were discussed. PMID:26207373

Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations.

Science.gov (United States)

Saville, Amanda; Charles, Melodi; Chavan, Suchitra; Muñoz, Miguel; Gómez-Alpizar, Luis; Ristaino, Jean Beagle

2017-12-01

Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.

Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

Science.gov (United States)

Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

2014-01-01

The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

Direct reciprocity in structured populations.

Science.gov (United States)

van Veelen, Matthijs; García, Julián; Rand, David G; Nowak, Martin A

2012-06-19

Reciprocity and repeated games have been at the center of attention when studying the evolution of human cooperation. Direct reciprocity is considered to be a powerful mechanism for the evolution of cooperation, and it is generally assumed that it can lead to high levels of cooperation. Here we explore an open-ended, infinite strategy space, where every strategy that can be encoded by a finite state automaton is a possible mutant. Surprisingly, we find that direct reciprocity alone does not lead to high levels of cooperation. Instead we observe perpetual oscillations between cooperation and defection, with defection being substantially more frequent than cooperation. The reason for this is that "indirect invasions" remove equilibrium strategies: every strategy has neutral mutants, which in turn can be invaded by other strategies. However, reciprocity is not the only way to promote cooperation. Another mechanism for the evolution of cooperation, which has received as much attention, is assortment because of population structure. Here we develop a theory that allows us to study the synergistic interaction between direct reciprocity and assortment. This framework is particularly well suited for understanding human interactions, which are typically repeated and occur in relatively fluid but not unstructured populations. We show that if repeated games are combined with only a small amount of assortment, then natural selection favors the behavior typically observed among humans: high levels of cooperation implemented using conditional strategies.

Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.

Directory of Open Access Journals (Sweden)

Jonas I Liechti

2017-08-01

Full Text Available Intense use of antibiotics for the treatment of diseases such as tuberculosis, malaria, Staphylococcus aureus or gonorrhea has led to rapidly increasing population levels of drug resistance. This has generally necessitated a switch to new drugs and the discontinuation of older ones, after which resistance often only declines slowly or even persists indefinitely. These long-term effects are usually ascribed to low fitness costs of resistance in absence of the drug. Here we show that structure in the host population, in particular heterogeneity in number of contacts, also plays an important role in the reversion dynamics. Host contact structure acts both during the phase of intense treatment, leading to non-random distributions of the resistant strain among the infected population, and after the discontinuation of the drug, by affecting the competition dynamics resulting in a mitigation of fitness advantages. As a consequence, we observe both a lower rate of reversion and a lower probability that reversion to sensitivity on the population level occurs after treatment is stopped. Our simulations show that the impact of heterogeneity in the host structure is maximal in the biologically most plausible parameter range, namely when fitness costs of resistance are small.

Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish.

Science.gov (United States)

Coleman, R A; Gauffre, B; Pavlova, A; Beheregaray, L B; Kearns, J; Lyon, J; Sasaki, M; Leblois, R; Sgro, C; Sunnucks, P

2018-01-12

Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (F ST  = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.

Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

Science.gov (United States)

Pressoir, G; Berthaud, J

2004-02-01

To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

Population assessment and degree of threat of chalybea Macrocarpa (Melastomataceae) endemic species from Colombia

International Nuclear Information System (INIS)

Gil Leguizamon, Pablo Andres; Morales Puentes, Maria Eugenia; Diaz Perez, Carlos Nelson

2014-01-01

Population assessment results from chalybea macrocarpaare shown, the specie is considerate ENDANGERED (EN) by its restricted area, threatened is generated by crops and extensive cattle farming. the study was conducted in the Boyaca Department (Colombia), Municipality of Arcabuco, in three established localities using herbarium and literature information; field work made possible identified distribution, density and phenology like sub criteria, allowing identify the presence extension and occupancy area. We took structural data (height, coverage and DBH) to determinate the population age's classes. Which the gathered information and the associated vegetation, the specie is re-categorized which the b IUCN criteria. It is distributed to the northwest and southern in Arcabuco, in an area of 59.9 km"2, 4 km"2 of occupancy and a population density of 50 individual/km"2. Flowering and fruiting is continuous through the year, however, most of the flowering is from March to August and fruiting from September to February. Age structure allows identified ten species between seedlings, juveniles and adults. Population is represented by few seedling individuals (10.6 %) and juveniles (20.9 %) versus adults (68.5 %). finally, C. macrocarpais upgraded to Critical Risk (CR B1ab (iii)).

Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

Science.gov (United States)

Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

2015-08-01

The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove

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.

Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae).

Science.gov (United States)

Mehner, Thomas; Pohlmann, Kirsten; Elkin, Che; Monaghan, Michael T; Nitz, Barbara; Freyhof, Jörg

2010-03-29

Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex), examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae). AFLP demonstrated a significant population structure (Bayesian thetaB = 0.22). Lower differentiation between allopatric (thetaB = 0.028) than sympatric (0.063-0.083) populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises the possibility that multiple lineages may be

Population structure and genetic trends for indigenous African beef ...

African Journals Online (AJOL)

The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...

Comparison of the population structure and life-history parameters ...

African Journals Online (AJOL)

Blacktail seabream Diplodus capensis were sampled from proximate (10 km apart) exploited and unexploited areas in southern Angola to compare their population structures and life-history parameters. Females dominated the larger size and older age classes in the unexploited area. In the exploited area the length and ...

Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

Science.gov (United States)

Hruschka, Daniel J; Hadley, Craig; Brewis, Alexandra A; Stojanowski, Christopher M

2015-01-01

Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28). However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74). Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

Directory of Open Access Journals (Sweden)

Daniel J Hruschka

Full Text Available Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28. However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74. Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

Job satisfaction of extension agents towards innovation ...

African Journals Online (AJOL)

The study assessed job satisfaction of extension agents towards innovation dissemination to fish farmers in Lagos State, Nigeria. A simple random sampling technique was used to select 44 extension officers from which data were collected. A structured questionnaire consisting of 6 personal characteristics, 23 management ...

History and Structure of Sub-Saharan Populations of Drosophila melanogaster

OpenAIRE

Pool, John E.; Aquadro, Charles F.

2006-01-01

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of geneti...

Age, growth and population structure of invasive lionfish (Pterois volitans/miles in northeast Florida using a length-based, age-structured population model

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Eric G. Johnson

2016-12-01

Full Text Available The effective management of invasive species requires detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish (Pterois volitans/miles have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1 lionfish exhibited rapid growth with seasonal variation in growth rates; (2 distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3 the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water.

Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model.

Science.gov (United States)

Johnson, Eric G; Swenarton, Mary Katherine

2016-01-01

The effective management of invasive species requires detailed understanding of the invader's life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish ( Pterois volitans/miles ) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water.

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

Advancing population ecology with integral projection models: a practical guide

DEFF Research Database (Denmark)

Merow, Cory; Dahlgren, Johan; Metcall, C. Jessica E.

2014-01-01

(e.g., environment). By combining regressions of vital rates, an IPM provides mechanistic insight into emergent ecological patterns such as population dynamics, species geographic distributions, or life history strategies. Here, we review important resources for building IPMs and provide...... a comprehensive guide, with extensive R code, for their construction. IPMs can be applied to any stage-structured population; here we illustrate IPMs for a series of plant life histories of increasing complexity and biological realism, highlighting the utility of various regression methods for capturing...

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization

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Ramona-Elena Irimia

2017-08-01

Full Text Available Centaurea solstitialis L. (yellow starthistle, Asteraceae is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C. solstitialis had been reported to be diploid (2n = 2x = 16 chromosomes, however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C. solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg, with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C. solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.

Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization.

Science.gov (United States)

Irimia, Ramona-Elena; Montesinos, Daniel; Eren, Özkan; Lortie, Christopher J; French, Kristine; Cavieres, Lohengrin A; Sotes, Gastón J; Hierro, José L; Jorge, Andreia; Loureiro, João

2017-01-01

Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C . solstitialis had been reported to be diploid (2 n  = 2 x  = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C . solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C . solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.

Population structure from NOS genes correlates with geographical differences in coronary incidence across Europe.

Science.gov (United States)

Carreras-Torres, Robert; Ferran, Albert; Zanetti, Daniela; Esteban, Esther; Varesi, Laurent; Pojskic, Naris; Coia, Valentina; Chaabani, Hassen; Via, Marc; Moral, Pedro

2016-12-01

The population analysis of cardiovascular risk and non-risk genetic variation can help to identify adaptive or random demographic processes that shaped coronary incidence variation across geography. In this study, 114 single nucleotide polymorphisms and 17 tandem repeat polymorphisms from Nitric Oxide Synthases (NOS) regions were analyzed in 1686 individuals from 35 populations from Europe, North Africa, and the Middle East. NOS genes encode for key enzymes on nitric oxide availability, which is involved in several cardiovascular processes. These genetic variations were used to test for selection and to infer the population structure of NOS regions. Moreover, we tested whether the variation in the incidence of coronary events and in the levels of classical risk factors in 11 of these European populations could be explained by the population structure estimates. Our results supported, first, the absence of clear signs of selection for NOS genetic variants associated with cardiovascular diseases, and second, the presence of a continuous genetic pattern of variation across European and North African populations without a Mediterranean barrier for gene flow. Finally, population structure estimates from NOS regions are closely correlated with coronary event rates and classical risk parameters (explaining 39-98%) among European populations. Our results reinforce the hypothesis that genetic bases of cardiovascular diseases and associated complex phenotypes could be geographically shaped by random demographic processes. © 2016 Wiley Periodicals, Inc.

Relationships between crustal structure and extension in the Basin and Range Province and East Africa

Energy Technology Data Exchange (ETDEWEB)

Keller, G R [University of Oklahoma, School of Geology and Geophysics, Norman, Oklahoma, 73019 (United States)], E-mail: grkeller@ou.edu

2008-07-01

The Basin and Range Province of the western United States and northern Mexico is often cited as a classic example of a wide rift. It is also a region where metamorphic core complexes such as the ones observed in the Aegean region are observed. On the other hand, the eastern arm (Kenya rift) of the East African rift is considered to be the classic example of a continental rift, which is by some definitions narrow. In this paper, these two features are briefly compared in terms of crustal structure and associated manifestations of extension.

Genetic population structure in an equatorial sparrow: roles for culture and geography.

Science.gov (United States)

Danner, J E; Fleischer, R C; Danner, R M; Moore, I T

2017-06-01

Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

Science.gov (United States)

Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

2011-02-01

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

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.

Pulses of movement across the sea ice: population connectivity and temporal genetic structure in the arctic fox.

Science.gov (United States)

Norén, Karin; Carmichael, Lindsey; Fuglei, Eva; Eide, Nina E; Hersteinsson, Pall; Angerbjörn, Anders

2011-08-01

Lemmings are involved in several important functions in the Arctic ecosystem. The Arctic fox (Vulpes lagopus) can be divided into two discrete ecotypes: "lemming foxes" and "coastal foxes". Crashes in lemming abundance can result in pulses of "lemming fox" movement across the Arctic sea ice and immigration into coastal habitats in search for food. These pulses can influence the genetic structure of the receiving population. We have tested the impact of immigration on the genetic structure of the "coastal fox" population in Svalbard by recording microsatellite variation in seven loci for 162 Arctic foxes sampled during the summer and winter over a 5-year period. Genetic heterogeneity and temporal genetic shifts, as inferred by STRUCTURE simulations and deviations from Hardy-Weinberg proportions, respectively, were recorded. Maximum likelihood estimates of movement as well as STRUCTURE simulations suggested that both immigration and genetic mixture are higher in Svalbard than in the neighbouring "lemming fox" populations. The STRUCTURE simulations and AMOVA revealed there are differences in genetic composition of the population between summer and winter seasons, indicating that immigrants are not present in the reproductive portion of the Svalbard population. Based on these results, we conclude that Arctic fox population structure varies with time and is influenced by immigration from neighbouring populations. The lemming cycle is likely an important factor shaping Arctic fox movement across sea ice and the subsequent population genetic structure, but is also likely to influence local adaptation to the coastal habitat and the prevalence of diseases.

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

Science.gov (United States)

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.

STRUCTURE, GROWTH AND MORPHOLOGY OF FISH POPULATIONS FROM GRAVEL-PIT VUKOVINA

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Ivan Jakovlić

2001-12-01

Full Text Available After the structure of fish populations from gravel-pit Vukovina was determined, those populations were checked for 10 morphometric and 4 meristic parameters, as well as for length-mass relationship. For chub (Leuciscus cephalus and pumpkinseed (Lepomis gibbosus some meristic characters expressed the values beyond those mentioned in the standard key for the freshwater fish species determination. When compared to other locations, length-mass relationship and condition factor (CF were significantly lower for all checked populations. This indicates that gravel-pit Vukovina is extremely oligotrophic and has very poor fish production.

Dispersal and population structure of a New World predator, the army ant Eciton burchellii

DEFF Research Database (Denmark)

Berghoff, S M; Kronauer, D J C; Edwards, K J

2008-01-01

barriers, which might have severe impacts on population structure and lead to population decline. Using nuclear microsatellite markers and mitochondrial sequences, we investigated genetic differentiation in a fragmented population in the Panama Canal area. While nuclear markers showed little...

Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds.

Science.gov (United States)

Selepe, Mokhethi Matthews; Ceccobelli, Simone; Lasagna, Emiliano; Kunene, Nokuthula Winfred

2018-01-01

The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

Genetic structure of South African Nguni (Zulu sheep populations reveals admixture with exotic breeds.

Directory of Open Access Journals (Sweden)

Mokhethi Matthews Selepe

Full Text Available The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69 and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

EXPORT STRUCTURE AT THE EXTENSIVE AND INTENSIVEMARGINS: THE CASE OF EMERGING ECONOMIES

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Gulcin Elif Yucel

2012-07-01

Full Text Available There is a consensus that increased exports have some benefits by enablingcountries to generate more revenue. But rather than exporting more, how acountry achieves high export performance is a more important question. Recentempirical literature highlights that intensive and extensive margins have differentcontributions to the export growth. Thus, export structure across the countries andproducts differs according to the effects of these margins. Developed countrieshave lost market share in goods exports to emerging economies, especially China.In other words, the reason of this loss of market share by most advancedeconomies is the increase in exports from emerging economies. In this study, wewill focus on the export structure of Turkey-as well as Brazil, China, India,Mexico and Russia (BCIMRT as benchmark countries-by providing a detailedanalysis of which areas of goods contribute to the intensive and/or extensivemargin growth and which margin dominates. In this study, ISIC Rev.3 4-digitlevel trade data is used which is available at the United Nations Commodity TradeStatistics (COMTRADE database for 2000-2010 period. By using descriptivestatistics on BCIMRT’s exports to the world, we decompose trade into itsextensive and intensive margins and try to answer whether export has increasedmost through new partnerships or through expanding existing trade flows in theseselected emerging economies.

Assessment of Genetic Heterogeneity in Structured Plant Populations Using Multivariate Whole-Genome Regression Models.

Science.gov (United States)

Lehermeier, Christina; Schön, Chris-Carolin; de Los Campos, Gustavo

2015-09-01

Plant breeding populations exhibit varying levels of structure and admixture; these features are likely to induce heterogeneity of marker effects across subpopulations. Traditionally, structure has been dealt with as a potential confounder, and various methods exist to "correct" for population stratification. However, these methods induce a mean correction that does not account for heterogeneity of marker effects. The animal breeding literature offers a few recent studies that consider modeling genetic heterogeneity in multibreed data, using multivariate models. However, these methods have received little attention in plant breeding where population structure can have different forms. In this article we address the problem of analyzing data from heterogeneous plant breeding populations, using three approaches: (a) a model that ignores population structure [A-genome-based best linear unbiased prediction (A-GBLUP)], (b) a stratified (i.e., within-group) analysis (W-GBLUP), and (c) a multivariate approach that uses multigroup data and accounts for heterogeneity (MG-GBLUP). The performance of the three models was assessed on three different data sets: a diversity panel of rice (Oryza sativa), a maize (Zea mays L.) half-sib panel, and a wheat (Triticum aestivum L.) data set that originated from plant breeding programs. The estimated genomic correlations between subpopulations varied from null to moderate, depending on the genetic distance between subpopulations and traits. Our assessment of prediction accuracy features cases where ignoring population structure leads to a parsimonious more powerful model as well as others where the multivariate and stratified approaches have higher predictive power. In general, the multivariate approach appeared slightly more robust than either the A- or the W-GBLUP. Copyright © 2015 by the Genetics Society of America.

Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

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Guillermo Velo-Antón

Full Text Available The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa. We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4 and microsatellite markers (32 loci and a subset of 12 loci. Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24 with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

Ontogenetic niche shifts and evolutionary branching in size-structured populations

NARCIS (Netherlands)

Claessen, D.; Dieckmann, U.

2002-01-01

There are many examples of size-structured populations where individuals sequentially exploit several niches in the course of their life history. Efficient exploitation of such ontogenetic niches generally requires specific morphological adaptations. Here, we study the evolutionary implications of

Intraspecific phytochemical variation shapes community and population structure for specialist caterpillars.

Science.gov (United States)

Glassmire, Andrea E; Jeffrey, Christopher S; Forister, Matthew L; Parchman, Thomas L; Nice, Chris C; Jahner, Joshua P; Wilson, Joseph S; Walla, Thomas R; Richards, Lora A; Smilanich, Angela M; Leonard, Michael D; Morrison, Colin R; Simbaña, Wilmer; Salagaje, Luis A; Dodson, Craig D; Miller, Jim S; Tepe, Eric J; Villamarin-Cortez, Santiago; Dyer, Lee A

2016-10-01

Chemically mediated plant-herbivore interactions contribute to the diversity of terrestrial communities and the diversification of plants and insects. While our understanding of the processes affecting community structure and evolutionary diversification has grown, few studies have investigated how trait variation shapes genetic and species diversity simultaneously in a tropical ecosystem. We investigated secondary metabolite variation among subpopulations of a single plant species, Piper kelleyi (Piperaceae), using high-performance liquid chromatography (HPLC), to understand associations between plant phytochemistry and host-specialized caterpillars in the genus Eois (Geometridae: Larentiinae) and associated parasitoid wasps and flies. In addition, we used a genotyping-by-sequencing approach to examine the genetic structure of one abundant caterpillar species, Eois encina, in relation to host phytochemical variation. We found substantive concentration differences among three major secondary metabolites, and these differences in chemistry predicted caterpillar and parasitoid community structure among host plant populations. Furthermore, E. encina populations located at high elevations were genetically different from other populations. They fed on plants containing high concentrations of prenylated benzoic acid. Thus, phytochemistry potentially shapes caterpillar and wasp community composition and geographic variation in species interactions, both of which can contribute to diversification of plants and insects. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

Science.gov (United States)

Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

2016-01-01

The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda

Science.gov (United States)

Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D.; Goffredo, Stefano

2015-01-01

Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa. PMID:26544963

An age-structured population balance model for microbial dynamics

Directory of Open Access Journals (Sweden)

Duarte M.V.E.

2003-01-01

Full Text Available This work presents an age-structured population balance model (ASPBM for a bioprocess in a continuous stirred-tank fermentor. It relates the macroscopic properties and dynamic behavior of biomass to the operational parameters and microscopic properties of cells. Population dynamics is governed by two time- and age-dependent density functions for living and dead cells, accounting for the influence of substrate and dissolved oxygen concentrations on cell division, aging and death processes. The ASPBM described biomass and substrate oscillations in aerobic continuous cultures as experimentally observed. It is noteworthy that a small data set consisting of nonsegregated measurements was sufficient to adjust a complex segregated mathematical model.

Genetic structure and diversity within and among six populations of ...

African Journals Online (AJOL)

Yomi

2010-04-24

Apr 24, 2010 ... Genetic structure and diversity within and among six populations of .... Lyopholized samples were ground to a fine powder. DNA extraction ..... 22(3): 287-292. Pei YL, Zou, YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995).

A Spatial Framework for Understanding Population Structure and Admixture.

Science.gov (United States)

Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M

2016-01-01

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

Polygyny and strong genetic structuring within an isolated population of the wood ant Formica rufa

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Wouter Dekoninck

2014-12-01

Full Text Available Social structuring of populations within some Formica species exhibits considerable variation going from monodomous and monogynous populations to polydomous, polygynous populations. The wood ant species Formica rufa appears to be mainly monodomous and monogynous throughout most of its distribution area in central and northern Europe. Only occasionally it was mentioned that F. rufa can have both polygynous and monogynous colonies in the same geographical region. We studied an isolated polydomous F. rufa population in a deciduous mixed forest in the north-west of Belgium. The level of polydomy within the colonies varied from monodomous to 11 nests per colony. Our genetic analysis of eight variable microsatellites suggest an oligo- to polygynous structure for at least the major part of the sampled nests. Relatedness amongst nest mate workers varies considerable within the population and colonies but confirms in general a polygynous structure. Additionally high genetic diversity (e.g. up to 8 out of 11 alleles per nest for the most variable locus and high within nest genetic variance (93% indicate that multiple queens contribute to the gene pool of workers of the same nest. Moreover significant genetic structuring among colonies indicates that gene flow between colonies is restricted and that exchange of workers between colonies is very limited. Finally we explain how possible factors as budding and the absence of Serviformica can explain the differences in genetic structure within this polygynous F. rufa population.

Multiple origins of outbreak populations of a native insect pest in an agro-ecosystem.

Science.gov (United States)

Kobayashi, T; Sakurai, T; Sakakibara, M; Watanabe, T

2011-06-01

Native insects can become epidemic pests in agro-ecosystems. A population genetics approach was applied to analyze the emergence and spread of outbreak populations of native insect species. Outbreaks of the mirid bug, Stenotus rubrovittatus, have rapidly expanded over Japan within the last two decades. To characterize the outbreak dynamics of this species, the genetic structure of local populations was assessed using polymorphisms of the mtDNA COI gene and six microsatellite loci. Results of the population genetic analysis suggested that S. rubrovittatus populations throughout Japan were genetically isolated by geographic distance and separated into three genetic clusters occupying spatially segregated regions. Phylogeographic analysis indicated that the genetic structure of S. rubrovittatus reflected post-glacial colonization. Early outbreaks of S. rubrovittatus in the 1980s occurred independently of genetically isolated populations. The genetic structure of the populations did not fit the pattern of an outbreak expansion, and therefore the data did not support the hypothesis that extensive outbreaks were caused by the dispersal of specific pestiferous populations. Rather, the historical genetic structure prior to the outbreaks was maintained throughout the increase in abundance of the mirid bug. Our study indicated that changes in the agro-environment induced multiple outbreaks of native pest populations. This implies that, given suitable environmental conditions, local populations may have the potential to outbreak even without invasion of populations from other environmentally degraded areas.

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.

Effect of dietary monensin on the bacterial population structure of dairy cattle colonic contents.

Science.gov (United States)

McGarvey, Jeffery A; Hamilton, Scott W; DePeters, Edward J; Mitloehner, Frank M

2010-02-01

To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the bacterial population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day(-1)) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their bacterial population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the bacterial population structure within the bovine gastrointestinal tract, we were unable to identify any significant difference in the bacterial population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level.

Genetic structure and diversity of three Colombian southwest afrodescendent populations using 8 STR's

International Nuclear Information System (INIS)

Guauque Olarte, Sandra; Fuentes Pardo, Angela Patricia; Cardenas Henao, Heiber; Barreto, Guillermo

2010-01-01

To estimate the diversity, structure and genetic flow in three Colombian southwest afrodescendent populations (Buenaventura, Mulalo y Tumaco), the alleles revealed by 8 autosomal STR's were analyzed in 78 no-related individuals, by the use of PCR and comparison with specific allelic ladders for every system resolved by polyacrylamide gel (8%). the results were compared with 2 Amerindian populations (Awa-Kuaikier and Coyaima) and 2 mixed Colombian populations (Valle del Cauca and Cauca). For the afrodescendent and Amerindian populations was found moderate diversity (h between 0.768±0.414 and 0.796±0.424), in contrast, the mixed population showed higher rates (>0.803), which is probably caused by mixing with Amerindians, that also can explain the high endogamy seen in mixed populations. The AMOVA exhibited moderate genetic structure between the afrodescendent populations (FST= 0.098; p<0.05), but higher between the three ethnical groups compared (FST=0.26723; p<0.05). The closer genetics distances are in favor of Tumaco and Buenaventura, supported for the migration rate found (34.298), which was the same inside of Amerindian and mixed populations. Maybe, because Mulalo is a closed isolated population, its differences in front others afrodescendent populations are explained. The neighbor-joining tree showed nearest relations among Amerindian and mixed populations, furthermore, the ancestral character for the afrodescendents. That sustains the idea of genetic flow maintained between the 3 ethnical groups, principally between Amerindian and mixed populations, supported because the genetic differences, migration rates and Amerindian matrilineality reported in the literature

Individual and Group Extension Methods: Perspectives from Vi ...

African Journals Online (AJOL)

Participatory Rural Appraisals (PRAs) tools including semi-structured questionnaires were administrated to 90 randomly selected farmers who had received extension services from the project. In addition, twelve project extension workers were interviewed. Data were analysed using SPSS computer package and descriptive ...

POPULATION STRUCTURE AND SPATIAL DISTRIBUTION OF Ceratozamia mexicana BRONGN. (ZAMIACEAE IN PRESERVED AND DISTURBED ENVIRONMENTS

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Andrés Rivera-Fernández

2012-11-01

Full Text Available Vegetal populations are affected by biotic and abiotic factors that influence the regeneration processes. The aims of this study were to know the population structure of Ceratozamia mexicana under two contrasting conditions (conserved site and disturbed site, and to determine if the sexual structure, the population density and the spatial distribution of C. mexicana are modified by effect of disturbance. Eight plots of 25 m2 within each site (conserved and disturbed were used. The structure and spatial distribution of the sites were determined. Methods included analysis of variance, spatial distribution indexes, and climatic and edaphic factors determined by conventional methods for their comparison. The conserved site showed a demographic structure of an inverted "J", while the disturbed site varied slightly with more discontinuous distribution. Population density was 0.78 individuals/m2 in the conserved site and 0.26 individuals/m2 in the disturbed site. Spatial distribution for all development stages of the plant was random, with the exception of the seedling stage, which was aggregated. Results showed that perturbation decreases the density of plants and removes reproductive individuals, which threatens the persistence of the population.

Prospective of the agricultural extension in Colombia

International Nuclear Information System (INIS)

David Hinestrosa, A.

1998-01-01

The situation of the agricultural extension is described in next twenty years, together with the regional programs of investigation and technology transfer, based in the rational use of the natural resources, the exploitation of markets, the former evaluation before and the expert systems. It proves the dynamic participation of producing leaders and their operation inside an outline of decentralization, privatization, sustainability, competitiveness, justness and invigoration and rural signification. It is supposed that the extension rural functional, bound to the investigation processes, transfer, development, technological development and markets. Institutionally it is expected that the extension is a service of regional and private character with an opportune and enough assignment of resources for the improvement of the quality of the rural population's life

Population structure and cultural geography of a folktale in Europe

Science.gov (United States)

Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

2013-01-01

Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

Global population structure and demographic history of the grey seal

DEFF Research Database (Denmark)

Klimova, A.; Phillips, C. D.; Fietz, Katharina

2014-01-01

Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat...... a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes...

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...

User-Extensible Graphics Using Abstract Structure,

Science.gov (United States)

1987-08-01

Flex 6 The Algol68 model of the graphical abstract structure 5 The creation of a PictureDefinition 6 The making of a picture from a PictureDefinition 7...data together with the operations that can be performed on that data. i 7! ś I _ § 4, The Alqol68 model of the graphical abstract structure Every

The role of population inertia in predicting the outcome of stage-structured biological invasions.

Science.gov (United States)

Guiver, Chris; Dreiwi, Hanan; Filannino, Donna-Maria; Hodgson, Dave; Lloyd, Stephanie; Townley, Stuart

2015-07-01

Deterministic dynamic models for coupled resident and invader populations are considered with the purpose of finding quantities that are effective at predicting when the invasive population will become established asymptotically. A key feature of the models considered is the stage-structure, meaning that the populations are described by vectors of discrete developmental stage- or age-classes. The vector structure permits exotic transient behaviour-phenomena not encountered in scalar models. Analysis using a linear Lyapunov function demonstrates that for the class of population models considered, a large so-called population inertia is indicative of successful invasion. Population inertia is an indicator of transient growth or decline. Furthermore, for the class of models considered, we find that the so-called invasion exponent, an existing index used in models for invasion, is not always a reliable comparative indicator of successful invasion. We highlight these findings through numerical examples and a biological interpretation of why this might be the case is discussed. Copyright © 2015. Published by Elsevier Inc.

An agent-based computational model for tuberculosis spreading on age-structured populations

Science.gov (United States)

Graciani Rodrigues, C. C.; Espíndola, Aquino L.; Penna, T. J. P.

2015-06-01

In this work we present an agent-based computational model to study the spreading of the tuberculosis (TB) disease on age-structured populations. The model proposed is a merge of two previous models: an agent-based computational model for the spreading of tuberculosis and a bit-string model for biological aging. The combination of TB with the population aging, reproduces the coexistence of health states, as seen in real populations. In addition, the universal exponential behavior of mortalities curves is still preserved. Finally, the population distribution as function of age shows the prevalence of TB mostly in elders, for high efficacy treatments.

Microsatellite markers to determine population genetic structure in the golden anchovy, Coilia dussumieri.

Science.gov (United States)

Kathirvelpandian, A; Gopalakrishnan, A; Lakra, W S; Krishna, Gopal; Sharma, Rupam; Musammilu, K K; Basheer, V S; Jena, J K

2014-06-01

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

Science.gov (United States)

Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

2018-01-01

Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123

46 CFR 176.675 - Extension of examination intervals.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Extension of examination intervals. 176.675 Section 176... 100 GROSS TONS) INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 176.675 Extension of examination intervals. The intervals between drydock examinations and internal structural examinations...

Death Valley turtlebacks: Mesozoic contractional structures overprinted by Cenozoic extension and metamorphism beneath syn-extensional plutons

Science.gov (United States)

Pavlis, T. L.; Miller, M.; Serpa, L.

2008-07-01

-thrust belts. Our work to the east of Death Valley suggests these thrusts were part of a NW trending thrust system that overprinted an older NE trending fold-thrust system that tracks into the Death Valley region from Nevada. These NW trending thrusts probably underlie all of the southern Black Mountains (south of the turtlebacks) and we suggest that pre-extensional structural relief along these basement thrusts placed basement at shallow crustal levels throughout what is now the Black Mountains; a conclusion consistent with the absence of rocks younger than Cambrian beneath Tertiary unconformities throughout the southern Death Valley region. In Late Miocene time, a major detachment system formed and the turtlebacks represent a mid-crustal shear zone developed during that time period, but this system is older, and structurally beneath younger detachments systems that comprise the Amargosa fault system. During motion on the detachment, an ~2km thick plutonic sheet was emplaced along the shear zone forming the Miocene plutonic assemblages of the Black Mountains, and produced upper amphibolite facies metamorphic assemblages along the floor of the pluton in what are now the Copper Canyon and Mormon Point turtlebacks, but the Badwater Turtleback escaped this metamorphism due to a different structural position. Motion continued along the floor of the pluton but syn-extensional folding produced structural relief along folds with axes parallel to the extension direction. Ultimately a new detachment system cut obliquely across the older extensional system, removing the roof of the pluton, but cutting down to its floor in the turtlebacks. This fault system formed a complex detachment system updip in the famous 'Amargosa Chaos', and removing the entire cover sequence from the Black Mountains (~10-12km of crustal section). The turtlebacks are therefore a composite structure in which extension contemporaneous with folding, presumably as a result of distributed transcurrent motion during

Death Valley turtlebacks: Mesozoic contractional structures overprinted by Cenozoic extension and metamorphism beneath syn-extensional plutons

Energy Technology Data Exchange (ETDEWEB)

Pavlis, T L; Serpa, L [Department of Geological Sciences, University of Texas at El Paso, El Paso, TX 7996 (United States); Miller, M [Department of Geological Sciences, University of Oregon, Eugene, OR 97403 (United States)], E-mail: tlpavlis@utep.edu

2008-07-01

-thrust belts. Our work to the east of Death Valley suggests these thrusts were part of a NW trending thrust system that overprinted an older NE trending fold-thrust system that tracks into the Death Valley region from Nevada. These NW trending thrusts probably underlie all of the southern Black Mountains (south of the turtlebacks) and we suggest that pre-extensional structural relief along these basement thrusts placed basement at shallow crustal levels throughout what is now the Black Mountains; a conclusion consistent with the absence of rocks younger than Cambrian beneath Tertiary unconformities throughout the southern Death Valley region. In Late Miocene time, a major detachment system formed and the turtlebacks represent a mid-crustal shear zone developed during that time period, but this system is older, and structurally beneath younger detachments systems that comprise the Amargosa fault system. During motion on the detachment, an {approx}2km thick plutonic sheet was emplaced along the shear zone forming the Miocene plutonic assemblages of the Black Mountains, and produced upper amphibolite facies metamorphic assemblages along the floor of the pluton in what are now the Copper Canyon and Mormon Point turtlebacks, but the Badwater Turtleback escaped this metamorphism due to a different structural position. Motion continued along the floor of the pluton but syn-extensional folding produced structural relief along folds with axes parallel to the extension direction. Ultimately a new detachment system cut obliquely across the older extensional system, removing the roof of the pluton, but cutting down to its floor in the turtlebacks. This fault system formed a complex detachment system updip in the famous 'Amargosa Chaos', and removing the entire cover sequence from the Black Mountains ({approx}10-12km of crustal section). The turtlebacks are therefore a composite structure in which extension contemporaneous with folding, presumably as a result of distributed

Death Valley turtlebacks: Mesozoic contractional structures overprinted by Cenozoic extension and metamorphism beneath syn-extensional plutons

International Nuclear Information System (INIS)

Pavlis, T L; Serpa, L; Miller, M

2008-01-01

-thrust belts. Our work to the east of Death Valley suggests these thrusts were part of a NW trending thrust system that overprinted an older NE trending fold-thrust system that tracks into the Death Valley region from Nevada. These NW trending thrusts probably underlie all of the southern Black Mountains (south of the turtlebacks) and we suggest that pre-extensional structural relief along these basement thrusts placed basement at shallow crustal levels throughout what is now the Black Mountains; a conclusion consistent with the absence of rocks younger than Cambrian beneath Tertiary unconformities throughout the southern Death Valley region. In Late Miocene time, a major detachment system formed and the turtlebacks represent a mid-crustal shear zone developed during that time period, but this system is older, and structurally beneath younger detachments systems that comprise the Amargosa fault system. During motion on the detachment, an ∼2km thick plutonic sheet was emplaced along the shear zone forming the Miocene plutonic assemblages of the Black Mountains, and produced upper amphibolite facies metamorphic assemblages along the floor of the pluton in what are now the Copper Canyon and Mormon Point turtlebacks, but the Badwater Turtleback escaped this metamorphism due to a different structural position. Motion continued along the floor of the pluton but syn-extensional folding produced structural relief along folds with axes parallel to the extension direction. Ultimately a new detachment system cut obliquely across the older extensional system, removing the roof of the pluton, but cutting down to its floor in the turtlebacks. This fault system formed a complex detachment system updip in the famous 'Amargosa Chaos', and removing the entire cover sequence from the Black Mountains (∼10-12km of crustal section). The turtlebacks are therefore a composite structure in which extension contemporaneous with folding, presumably as a result of distributed transcurrent motion

Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

Science.gov (United States)

Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

2014-01-01

Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

Effects of growth curve plasticity on size-structured population dynamics

DEFF Research Database (Denmark)

Zhang, Lai; Lin, Zhigui; Pedersen, Michael

2011-01-01

The physiological-structured population models assume that a fixed fraction of energy intake is utilized for individual growth and maintenance while the remaining for adult fertility. The assumption results in two concerns: energy loss for juveniles and a reproduction dilemma for adults. The dile...

Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

Science.gov (United States)

Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

2016-04-01

Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pKenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. Copyright © 2015. Published by Elsevier B.V.

Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing.

Science.gov (United States)

Jo, Yeong Deuk; Choi, Yoomi; Kim, Dong-Hwan; Kim, Byung-Dong; Kang, Byoung-Cheorl

2014-07-04

Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Although large portion of sequence context was

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

Science.gov (United States)

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

A Genomic View of the Peopling and Population Structure of India

Science.gov (United States)

Majumder, Partha P.; Basu, Analabha

2015-01-01

Recent advances in molecular and statistical genetics have enabled the reconstruction of human history by studying living humans. The ability to sequence and study DNA by calibrating the rate of accumulation of changes with evolutionary time has enabled robust inferences about how humans have evolved. These data indicate that modern humans evolved in Africa about 150,000 years ago and, consistent with paleontological evidence, migrated out of Africa. And through a series of settlements, demographic expansions, and further migrations, they populated the entire world. One of the first waves of migration from Africa was into India. Subsequent, more recent, waves of migration from other parts of the world have resulted in India being a genetic melting pot. Contemporary India has a rich tapestry of cultures and ecologies. There are about 400 tribal groups and more than 4000 groups of castes and subcastes, speaking dialects of 22 recognized languages belonging to four major language families. The contemporary social structure of Indian populations is characterized by endogamy with different degrees of porosity. The social structure, possibly coupled with large ecological heterogeneity, has resulted in considerable genetic diversity and local genetic differences within India. In this essay, we provide genetic evidence of how India may have been peopled, the nature and extent of its genetic diversity, and genetic structure among the extant populations of India. PMID:25147176

CONTRIBUTIONS OF SEXUAL AND ASEXUAL REPRODUCTION TO POPULATION STRUCTURE IN THE CLONAL SOFT CORAL, ALCYONIUM RUDYI.

Science.gov (United States)

McFadden, Catherine S

1997-02-01

Numerous studies of population structure in sessile clonal marine invertebrates have demonstrated low genotypic diversity and nonequilibrium genotype frequencies within local populations that are monopolized by relatively few, highly replicated genets. All of the species studied to date produce planktonic sexual propagules capable of dispersing long distances; despite local genotypic disequilibria, populations are often panmictic over large geographic areas. The population structure paradigm these species represent may not be typical of the majority of clonal invertebrate groups, however, which are believed to produce highly philopatric sexual propagules. I used allozyme variation to examine the population structure of the temperate soft coral, Alcyonium rudyi, a typical clonal species whose sexually produced larvae and asexually produced ramets both have very low dispersal capabilities. Like other clonal plants and invertebrates, the local population dynamics of A. rudyi are dominated by asexual reproduction, and recruitment of new sexually produced genets occurs infrequently. As expected from its philopatric larval stage, estimates of genetic differentiation among populations of A. rudyi were highly significant at all spatial scales examined (mean θ = 0.300 among 20 populations spanning a 1100-km range), suggesting that genetic exchange seldom occurs among populations separated by as little as a few hundred meters. Mapping of multilocus allozyme genotypes within a dense aggregation of A. rudyi ramets confirmed that dispersal of asexual propagules is also very limited: members of the same genet usually remain within invertebrates, populations of A. rudyi do not appear to be dominated by a few widespread genets: estimates of genotypic diversity (G o ) within 20 geographically distinct populations did not differ from expectations for outcrossing, sexual populations. Despite theoretical suggestions that philopatric dispersal combined with typically small effective

Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

Science.gov (United States)

Cushing, J M; Henson, Shandelle M

2018-02-03

For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

Selection signatures in worldwide sheep populations.

Science.gov (United States)

Fariello, Maria-Ines; Servin, Bertrand; Tosser-Klopp, Gwenola; Rupp, Rachel; Moreno, Carole; San Cristobal, Magali; Boitard, Simon

2014-01-01

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.

Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

Science.gov (United States)

Pometti, Carolina; Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

2018-01-01

The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

Negative extensibility metamaterials: Occurrence and design-space topology

Science.gov (United States)

Karpov, Eduard G.; Danso, Larry A.; Klein, John T.

2017-08-01

A negative extensibility material structure pulls back and contracts when the external tensile load reaches a certain critical level. In this paper, we reveal basic mathematical features of the nonlinear strain energy function responsible for this unusual mechanical property. A systematic discussion leads to a comprehensive phase diagram in terms of design parameters for a simple unit cell structure that provides a panoramic view of all possible nonlinear mechanical behaviors. A negative extensibility region clearly is identified in the diagram. The sought property is seen to be rare, occurring only for a very narrow range of the design parameters. Nonetheless, due to the simplicity of the studied structure we suggest that the negative extensibility should be a more common phenomenon than previously thought. It can appear in simple bistable cells made of only several linearly elastic links, although at some peculiar combinations of their properties. These bistable unit cells can be used to design periodic mechanical metamaterials whose examples are shown as well as innovative architectural metastructures.

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.

Population structure, spatial distribution and life-history traits of blacktip reef sharks Carcharhinus melanopterus.

Science.gov (United States)

Mourier, J; Mills, S C; Planes, S

2013-03-01

During a survey of the population of blacktip reef shark Carcharhinus melanopterus in Moorea (French Polynesia) between 2007 and 2011, population structural characteristics were estimated from 268 individuals. Total length (LT ) ranged from 48 to 139 cm and 48 to 157 cm for males and females, respectively, demonstrating that the average LT of females was larger than that of males. The C. melanopterus population at Moorea showed an apparent spatial sexual segregation with females preferentially frequenting lagoons and males the fore-reefs. Mean growth rate was c. 6 cm year(-1) . Males reached sexual maturity at 111 cm LT . This study reports on the population characteristics of this widespread carcharhinid shark species and makes comparisons with other locations, confirming high geographic variability in the population structure of the species. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

Directory of Open Access Journals (Sweden)

Mobegi Victor A

2012-07-01

Full Text Available Abstract Background Malaria parasite population genetic structure varies among areas of differing endemicity, but this has not been systematically studied across Plasmodium falciparum populations in Africa where most infections occur. Methods Ten polymorphic P. falciparum microsatellite loci were genotyped in 268 infections from eight locations in four West African countries (Republic of Guinea, Guinea Bissau, The Gambia and Senegal, spanning a highly endemic forested region in the south to a low endemic Sahelian region in the north. Analysis was performed on proportions of mixed genotype infections, genotypic diversity among isolates, multilocus standardized index of association, and inter-population differentiation. Results Each location had similar levels of pairwise genotypic diversity among isolates, although there were many more mixed parasite genotype infections in the south. Apart from a few isolates that were virtually identical, the multilocus index of association was not significant in any population. Genetic differentiation between populations was low (most pairwise FST values  Conclusions Although proportions of mixed genotype infections varied with endemicity as expected, population genetic structure was similar across the diverse sites. Very substantial reduction in transmission would be needed to cause fragmented or epidemic sub-structure in this region.

Landlocked Arctic charr ( Salvelinus alpinus ) population structure and lake morphometry in Greenland - is there a connection?

DEFF Research Database (Denmark)

Riget, F.; Jeppesen, E.; Landkildehus, F.

2000-01-01

correlated with lake volume. Our study indicates that the charr population structure became more complex with increasing lake size. Moreover, the population structure seemed to be influenced by lake-water transparency and the presence or absence of three-spined stickleback (Gasterosteus aculeatus)...

Brief communication: Structural monitoring for lifetime extension of offshore wind monopiles: can strain measurements at one level tell us everything?

Directory of Open Access Journals (Sweden)

L. Ziegler

2017-09-01

Full Text Available Operators need accurate knowledge on structural reserves to decide about lifetime extension of offshore wind turbines. Load monitoring enables us to directly compare design loads with real loading histories of the support structure in order to calculate its remaining useful lifetime. Monitoring of every hot spot is technically and financially not feasible. This paper presents a novel idea for load monitoring of monopiles. It requires strain measurements at only one level convenient for sensor installation, such as tower bottom. Measurements are converted into damage equivalent loads for 10 min time intervals. Damage equivalent loads are extrapolated to other locations of the structure with a simulation model and statistical algorithm. For this, structural loads at all locations of the monopile are calculated with aero-hydro-elastic software and updated finite element models. Damage equivalent loads at unmeasured locations are predicted from the simulation results with a k-nearest neighbor regression algorithm. The extrapolation was tested with numerical simulations of an 8 MW offshore wind turbine. Results show that damage can be predicted with an error of 1–3 % if this is done conditional on mean wind speed, which is very promising. The load monitoring concept is simple, cheap and easy to implement. This makes it ideal for making decisions on lifetime extension of monopiles.

Population structure of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in China identified using microsatellites.

Science.gov (United States)

Cao, Jinjun; Li, Jie; Niu, Jianqun; Liu, Xiaoxia; Zhang, Qingwen

2012-04-01

The spiraea aphid (Aphis spiraecola Patch) is a primary pest of fruit trees, particularly pear trees in China. Despite the economic importance of this pest, little is known about its genetic structure or its patterns of dispersal at local and regional scales; however, knowledge of these characteristics is important for establishing effective control strategies for this pest. The genetic variability of 431 individuals from 21 populations on pear trees in China was investigated using eight polymorphic microsatellite loci. The high polymorphism of these markers was evident from the expected heterozygosity value (He = 0.824) and the Polymorphism Information Content (PIC = 0.805), indicating that the spiraea aphid maintains a high level of genetic diversity. The analysis of molecular variance revealed a middle level of population differentiation (F(ST) = 0.1478) among A. spiraecola populations. This result is consistent with the results of the STRUCTURE analysis (K = 3), the unweighted pair-group method with arithmetic average tree and the Mantel test (r = 0.6392; P < 0.05). Our results indicate high levels of genetic exchange in the spiraea aphid, possibly facilitated by geography and climate. Our findings emphasize the importance of considering regional differences in studies of population structure, even when strong isolation-by-distance influences the genetic population structure of species.

Experimental design and estimation of growth rate distributions in size-structured shrimp populations

International Nuclear Information System (INIS)

Banks, H T; Davis, Jimena L; Ernstberger, Stacey L; Hu, Shuhua; Artimovich, Elena; Dhar, Arun K

2009-01-01

We discuss inverse problem results for problems involving the estimation of probability distributions using aggregate data for growth in populations. We begin with a mathematical model describing variability in the early growth process of size-structured shrimp populations and discuss a computational methodology for the design of experiments to validate the model and estimate the growth-rate distributions in shrimp populations. Parameter-estimation findings using experimental data from experiments so designed for shrimp populations cultivated at Advanced BioNutrition Corporation are presented, illustrating the usefulness of mathematical and statistical modeling in understanding the uncertainty in the growth dynamics of such populations

assessment of extension agents' communication methods

African Journals Online (AJOL)

USER

communication, therefore, requires a balance between homophily and heterophily. ... Networks are structured fabrics of the organization made up of lines, .... work life affect work performance among government agriculture extension officers?

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): Natural replicate tests of post-Pleistocene evolution

Science.gov (United States)

Morris-Pocock, J. A.; Taylor, S.A.; Birt, T.P.; Damus, M.; Piatt, John F.; Warheit, K.I.; Friesen, Vicki L.

2008-01-01

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east-west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east-west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa. ?? 2008 The Authors.

Changes in population structures of the major species in selected ...

African Journals Online (AJOL)

The study was carried out in six satellite lakes by making investigations on fish collected from experimental and artisanal fisheries. The fishes were analysed for length frequencies, weight and numbers caught to determine the population structure of the fishes. Indiscriminate fishing by deploying illegal gears and increased ...

Cannibalism in a size-structured population: energy extraction and control

NARCIS (Netherlands)

Persson, L.; Claessen, D.; de Roos, A.M.; Byström, P.; Sjögren, S.; Svanbäck, R.; Wahlström, E.; Westman, E.

2004-01-01

Recent size-structured cannibalistic models point to the importance of the energy gain by cannibals and also show that this gain may result in the emergence of giant individuals. We use a combination of a 10-year field study of a perch (Perca fluviatilis) population and quantitative within-season

Cannibalism in a size-structured population: Enery extraction and control

NARCIS (Netherlands)

Persson, L.; Claessen, D.; de Roos, A.M.; Bystrom, P.; Sjogren, S.; Svanback, R.; Wahlstrom, E.; Westman, E.

2004-01-01

Recent size-structured cannibalistic models point to the importance of the energy gain by cannibals and also show that this gain may result in the emergence of giant individuals. We use a combination of a 10-year field study of a perch (Perca fluviatilis) population and quantitative within-season

The confounding effect of population structure on bayesian skyline plot inferences of demographic history

DEFF Research Database (Denmark)

Heller, Rasmus; Chikhi, Lounes; Siegismund, Hans

2013-01-01

Many coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading...... when it is violated. Among the most widely applied demographic inference methods are Bayesian skyline plots (BSPs), which are used across a range of biological fields. Violations of the panmixia assumption are to be expected in many biological systems, but the consequences for skyline plot inferences...... the best scheme for inferring demographic change over a typical time scale. Analyses of data from a structured African buffalo population demonstrate how BSP results can be strengthened by simulations. We recommend that sample selection should be carefully considered in relation to population structure...

Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

DEFF Research Database (Denmark)

Muwanka, V.B.; Nyakaana, S.; Siegismund, Hans Redlef

2007-01-01

populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection...

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

Science.gov (United States)

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat

Using Population Matrix Modeling to Predict AEGIS Fire Controlmen Community Structure

National Research Council Canada - National Science Library

McKeon, Thomas J

2007-01-01

.... A Population Matrix with Markov properties was used to develop the AEGIS FC aging model. The goal of this model was to provide an accurate predication of the future AEGIS FC community structure based upon variables...

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, 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

Directory of Open Access Journals (Sweden)

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

Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

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Mallikarjuna Rao eKovi

2015-11-01

Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

Temporal genetic population structure and interannual variation in migration behavior of Pacific Lamprey Entosphenus tridentatus

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Clemens, Benjamin J.; Wyss, Lance A.; McCoun, Rebecca; Courter, Ian; Schwabe, Lawrence; Peery, Christopher; Schreck, Carl B.; Spice, Erin K.; Docker, Margaret F.

2017-01-01

Studies using neutral loci suggest that Pacific lamprey, Entosphenus tridentatus, lack strong spatial genetic population structure. However, it is unknown whether temporal genetic population structure exists. We tested whether adult Pacific lamprey: (1) show temporal genetic population structure; and (2) migrate different distances between years. We non-lethally sampled lamprey for DNA in 2009 and 2010 and used eight microsatellite loci to test for genetic population structure. We used telemetry to record the migration behaviors of these fish. Lamprey were assignable to three moderately differentiated genetic clusters (FST = 0.16–0.24 for all pairwise comparisons): one cluster was composed of individuals from 2009, and the other two contained individuals from 2010. The FST value between years was 0.13 and between genetic clusters within 2010 was 0.20. A total of 372 (72.5%) fish were detected multiple times during their migrations. Most fish (69.9%) remained in the mainstem Willamette River; the remaining 30.1% migrated into tributaries. Eighty-two lamprey exhibited multiple back-and-forth movements among tributaries and the mainstem, which may indicate searching behaviors. All migration distances were significantly greater in 2010, when the amplitude of river discharge was greater. Our data suggest genetic structuring between and within years that may reflect different cohorts.

Extension in the City: Meeting the Challenges of Scale

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Jennifer Sarah Tiffany

2017-06-01

Full Text Available The urban share of the United States and global population has been climbing steadily since well before the inception of Extension. As of the 2010 census, more than four out of five U.S. residents lived in urban areas, with 71% of the total U.S. population living in cities with more than 50,000 residents, and 10% living in smaller urban clusters. Cornell University established Cooperative Extension offices in New York City (CUCE-NYC well after the Extension system was developed in rural and suburban counties throughout New York State. NYC is the largest city and part of the largest metropolitan area in the U.S., creating significant challenges of scale for Extension programming. The ratio of NYC residents to CUCE-NYC staff is roughly 125,000:1. CUCE-NYC works to mobilize limited resources to create large and positive impacts on individuals, families, communities, and institutions. Strategies to achieve these goals include partnership development, community recruitment, leadership development, and ecological efforts to foster setting-level change. Key CUCE-NYC strategies are grounded in sustained, intensive connections to communities, organizations, and other human ecological contexts. Geospatial mapping of program activities enables assessment and improvement of program reach and impact.

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

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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 size structure indices and growth standards for Salmo (trutta trutta Linnaeus, 1758 in Central Italy

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Pedicillo G.

2010-10-01

Full Text Available The purpose of this study was to provide reference data on the growth and population structure of brown trout Salmo (trutta trutta Linnaeus, in Central Italy. Standards for growth (percentiles and a standard growth model were developed from the von Bertalanffy growth model by using length-at-age data obtained from 122 sampling sites in the River Tiber basin. Length-frequency indices provide a numeric estimation for deviations of the population structure from a balanced population. We adapted the traditional North American Relative Stock Density (RSD and Proportional Stock Density (PSD indices to brown trout populations in Central Italy by means of two methods. In the first method, the benchmarks of length categories were established by using percentages applied to the largest individual in the dataset. In the second method, asymptotic length and size at maturity were used to define the length categories for index calculation. Both methods were tested on length-frequency data from 263 sampling sites in the River Tiber basin. The results showed that the PSD calculated by the first method provided a better insight into the population structures of brown trout. These results provide tools that will help ichthyologists and fish managers to compare the growth and population structure of brown trout throughout Central Italy.

Evolutionary mixed games in structured populations: Cooperation and the benefits of heterogeneity

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Amaral, Marco A.; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K. L.

2016-04-01

Evolutionary games on networks traditionally involve the same game at each interaction. Here we depart from this assumption by considering mixed games, where the game played at each interaction is drawn uniformly at random from a set of two different games. While in well-mixed populations the random mixture of the two games is always equivalent to the average single game, in structured populations this is not always the case. We show that the outcome is, in fact, strongly dependent on the distance of separation of the two games in the parameter space. Effectively, this distance introduces payoff heterogeneity, and the average game is returned only if the heterogeneity is small. For higher levels of heterogeneity the distance to the average game grows, which often involves the promotion of cooperation. The presented results support preceding research that highlights the favorable role of heterogeneity regardless of its origin, and they also emphasize the importance of the population structure in amplifying facilitators of cooperation.

Abundance, population structure and conservation of Podocnemis lewyana (Podocnemididae) at the Prado River, Colombia

International Nuclear Information System (INIS)

Gonzalez Zarate, Adriana; Montenegro, Olga; Castano Mora, Olga Victoria; Vargas Ramirez Mario

2014-01-01

Along the Prado River, at southeast of Colombia, there is a population of Podocnemis lewyana, an endemic and endangered river turtle. Relative abundance, population structure and conservation threats were determined using field data obtained in 2007 and 2009. Relative abundance was estimated by turtle catch per unit of time, which was used to compare between the two sampling years. Additionally, turtles per kilometer were counted in 2009 alone, to compare with other populations distributed in the north of the country. The population structure was determined by the frequency of individuals of several size classes and sex ratio of captured animals. Sexual dimorphism was examined in adult animals by morphometry. One hundred and ten turtles were captured in 2007 and 72 in 2009. The relative abundance of individuals observed was an averaged of 54.46 sightings/km representing the most abundant population of the country so far. The population's structure was characterized by a higher frequency of individuals of 21-30 cm maximum straight carapace length SCL and absence of individuals of less than 10 cm SCL or greater than 40 cm SCL. Sex ratio was 2.52:1 for 2007 and 2.75:1 for 2009, being higher for females. The main identified threats to the population of P. lewyana at Prado River were (i) alterations of habitat, (ii) changes in the natural flow of the river, (iii) the use of inappropriate fishing arts and (iv) probable interruption of migrations. Prado River is hereby proposed as priority area for further research and conservation of Podocnemis lewyana in the upper Magdalena River basin.

Study on risk insight for additional ILRT interval extension

International Nuclear Information System (INIS)

Seo, M. R.; Hong, S. Y.; Kim, M. K.; Chung, B. S.; Oh, H. C.

2005-01-01

In U.S., the containment Integrated Leakage Rate Test (ILRT) interval was extended from 3 times per 10 years to once per 10 years based on NUREG-1493 'Performance-Based Containment Leak-Test Program' in 1995. In September, 2001, ILRT interval was extended up to once per 15 years based on Nuclear Energy Industry (NEI) provisional guidance 'Interim Guidance for Performing Risk Impact Assessments In Support of One-Time Extensions for Containment Integrated Leakage Rate Test Surveillance Intervals'. In Korea, the containment ILRT was performed with 5 year interval. But, in MOST(Ministry of Science and Technology) Notice 2004-15 'Standard for the Leak- Rate Test of the Nuclear Reactor Containment', the extension of the ILRT interval to once per 10 year can be allowed if some conditions are met. So, the safety analysis for the extension of Yonggwang Nuclear (YGN) Unit 1 and 2 ILRT interval extension to once per 10 years was completed based on the methodology in NUREG-1493. But, during review process by regulatory body, KINS, it was required that some various risk insight or index for risk analysis should be developed. So, we began to study NEI interim report for 15 year ILRT interval extension. As previous analysis based on NUREG-1493, MACCS II (MELCOR Accident Consequence Code System) computer code was used for the risk analysis of the population, and the population dose was selected as a reference index for the risk evaluation

Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

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Maris Hindrikson

Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

[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%).

Evolutionary game dynamics in a growing structured population

Energy Technology Data Exchange (ETDEWEB)

Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza (Spain); Traulsen, Arne [Emmy-Noether Group for Evolutionary Dynamics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen (Germany)], E-mail: traulsen@evolbio.mpg.de

2009-08-15

We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

Evolutionary game dynamics in a growing structured population

International Nuclear Information System (INIS)

Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

2009-01-01

We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.

Science.gov (United States)

Hoh, Boon-Peng; Deng, Lian; Julia-Ashazila, Mat Jusoh; Zuraihan, Zakaria; Nur-Hasnah, Ma'amor; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Endom, Ismail; Zilfalil, Bin Alwi; Khalid, Yusoff; Xu, Shuhua

2015-07-22

Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

VAMPS: a website for visualization and analysis of microbial population structures.

Science.gov (United States)

Huse, Susan M; Mark Welch, David B; Voorhis, Andy; Shipunova, Anna; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

2014-02-05

The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 10⁵-10⁸ reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators' private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations.

Science.gov (United States)

Jackson, Matthew A; Bonder, Marc Jan; Kuncheva, Zhana; Zierer, Jonas; Fu, Jingyuan; Kurilshikov, Alexander; Wijmenga, Cisca; Zhernakova, Alexandra; Bell, Jordana T; Spector, Tim D; Steves, Claire J

2018-01-01

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river.

Science.gov (United States)

Olsen, J B; Beacham, T D; Wetklo, M; Seeb, L W; Smith, C T; Flannery, B G; Wenburg, J K

2010-04-01

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa.

Science.gov (United States)

Muzhinji, Norman; Woodhall, James W; Truter, Mariette; van der Waals, Jacquie E

2016-05-01

Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic diversity and structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analysed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intra-population genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes were identified with few shared among populations. Low levels of clonality (13-39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy-Weinberg equilibrium and all four populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in South Africa and results may help to develop knowledge-based disease management strategies. Copyright © 2016 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

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.

Homogenous Population Genetic Structure of the Non-Native Raccoon Dog (Nyctereutes procyonoides) in Europe as a Result of Rapid Population Expansion

Science.gov (United States)

Drygala, Frank; Korablev, Nikolay; Ansorge, Hermann; Fickel, Joerns; Isomursu, Marja; Elmeros, Morten; Kowalczyk, Rafał; Baltrunaite, Laima; Balciauskas, Linas; Saarma, Urmas; Schulze, Christoph; Borkenhagen, Peter; Frantz, Alain C.

2016-01-01

The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species’ dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large ‘central’ population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations. PMID:27064784

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

mtDNA variation in caste populations of Andhra Pradesh, India.

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Bamshad, M; Fraley, A E; Crawford, M H; Cann, R L; Busi, B R; Naidu, J M; Jorde, L B

1996-02-01

Various anthropological analyses have documented extensive regional variation among populations on the subcontinent of India using morphological, protein, blood group, and nuclear DNA polymorphisms. These patterns are the product of complex population structure (genetic drift, gene flow) and a population history noted for numerous branching events. As a result, the interpretation of relationships among caste populations of South India and between Indians and continental populations remains controversial. The Hindu caste system is a general model of genetic differentiation among endogamous populations stratified by social forces (e.g., religion and occupation). The mitochondrial DNA (mtDNA) molecule has unique properties that facilitate the exploration of population structure. We analyzed 36 Hindu men born in Andhra Pradesh who were unrelated matrilineally through at least 3 generations and who represent 4 caste populations: Brahmin (9), Yadava (10), Kapu (7), and Relli (10). Individuals from Africa (36), Asia (36), and Europe (36) were sampled for comparison. A 200-base-pair segment of hypervariable segment 2 (HVS2) of the mtDNA control region was sequenced in all individuals. In the Indian castes 25 distinct haplotypes are identified. Aside from the Cambridge reference sequence, only two haplotypes are shared between caste populations. Middle castes form a highly supported cluster in a neighbor-joining network. Mean nucleotide diversity within each caste is 0.015, 0.012, 0.011, and 0.012 for the Brahmin, Yadava, Kapu, and Relli, respectively. mtDNA variation is highly structured between castes (GST = 0.17; p caste populations of Andhra Pradesh cluster more often with Africans than with Asians or Europeans. This is suggestive of admixture with African populations.

Small-scale genetic structure in an endangered wetland specialist: possible effects of landscape change and population recovery

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van Rees, Charles B.; Reed, J. Michael; Wilson, Robert E.; Underwood, Jared G.; Sonsthagen, Sarah A.

2018-01-01

The effects of anthropogenic landscape change on genetic population structure are well studied, but the temporal and spatial scales at which genetic structure can develop, especially in taxa with high dispersal capabilities like birds, are less well understood. We investigated population structure in the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered wetland specialist bird on the island of O`ahu (Hawai`i, USA). Hawaiian gallinules have experienced a gradual population recovery from near extinction in the 1950s, and have recolonized wetlands on O`ahu in the context of a rapidly urbanizing landscape. We genotyped 152 Hawaiian gallinules at 12 microsatellite loci and sequenced a 520 base-pair fragment of the ND2 region of mitochondrial DNA (mtDNA) from individuals captured at 13 wetland locations on O`ahu in 2014–2016. We observed moderate to high genetic structuring (overall microsatellite FST = 0.098, mtDNA FST = 0.248) among populations of Hawaiian gallinules occupying wetlands at very close geographic proximity (e.g., 1.5–55 km). Asymmetry in gene flow estimates suggests that Hawaiian gallinules may have persisted in 2–3 strongholds which served as source populations that recolonized more recently restored habitats currently supporting large numbers of birds. Our results highlight that genetic structure can develop in taxa that are expanding their range after severe population decline, and that biologically significant structuring can occur over small geographic distances, even in avian taxa.

Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

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Moritz Robin FA

2003-05-01

Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

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Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

2015-01-01

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

Directory of Open Access Journals (Sweden)

Jian-Wei Zong