A5048187918- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Evolution and Genetic Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Marine animal studies overview
- Wildlife Ecology and Conservation
- Marine and fisheries research
- Species Distribution and Climate Change
- Fish Ecology and Management Studies
- Plant and animal studies
- Ecology and Vegetation Dynamics Studies
- Genetic Associations and Epidemiology
- Bayesian Methods and Mixture Models
- Marine and coastal plant biology
- Identification and Quantification in Food
- High Altitude and Hypoxia
- Marine Biology and Ecology Research
- Coral and Marine Ecosystems Studies
- Animal Ecology and Behavior Studies
- Botany and Plant Ecology Studies
- Evolution and Paleontology Studies
- Animal Behavior and Reproduction
- Avian ecology and behavior
- Metabolomics and Mass Spectrometry Studies
- Markov Chains and Monte Carlo Methods
University of St Andrews
2015-2024
Université de Moncton
2024
Natural History Museum
2024
Harvard University Press
2024
Sands
2014-2022
Scottish Association For Marine Science
2019
Centre National de la Recherche Scientifique
2008-2018
Laboratoire d'Écologie Alpine
2008-2018
Université Grenoble Alpes
2005-2018
Andrews University
2015-2018
Identifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects adaptive are based on locus-specific population differentiation coefficients identify outliers. Here we extend such an approach estimate directly the probability that each locus subject using a Bayesian method. We also it allow use dominant markers like AFLPs. It has been shown this model robust complex demographic scenarios for...
Table of contents Contributors Preface Introduction Chapter 1 Metapopulation biology: Past, present, and future 2 dynamics: Perspectives from landscape ecology 3 Continuous-space models for population dynamics 4 in highly fragmented landscapes 5 Application stochastic patch occupancy to real metapopulations 6 From metacommunities genetics 7 Selection drift 8 Metapopulations coalescent theory 9 quantitative genetics: The differentiation Evolutionary 10 Life history evolution 11...
Abstract Bayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex scenarios using genetic data. Articles presenting new generally include sensitivity that evaluate their performance, but tend be limited and need followed by a more thorough evaluation. Here we the performance recent method, bayesass , which allows estimation migration rates among populations, as well inbreeding coefficient each local...
The study of population genetic structure is a fundamental problem in biology because it helps us obtain deeper understanding the evolutionary process. One issues most assiduously studied this context assessment relative importance environmental factors (geographic distance, language, temperature, altitude, etc.) on populations. widely used method to address question multivariate Mantel test, nonparametric that calculates correlation coefficient between dependent matrix pairwise distances...
The emergence of farming during the Neolithic transition, including domestication livestock, was a critical point in evolution human kind. goat (Capra hircus) one first domesticated ungulates. In this study, we compared genetic diversity domestic goats to that modern representatives their wild ancestor, bezoar, by analyzing 473 samples collected over whole distribution range latter species. This partly confirms and significantly clarifies scenario already proposed archaeological evidence....
Genetic admixture of distinct gene pools is the consequence complex spatiotemporal processes that could have involved massive migration and local mating during history a species. However, current methods for estimating individual proportions lack incorporation such piece information. Here, we extend Bayesian clustering algorithms by including global trend surfaces spatial autocorrelation in prior distribution on coefficients. We test our algorithm using spatially explicit realistic...
Abstract The recent availability of next‐generation sequencing (NGS) has made possible the use dense genetic markers to identify regions genome that may be under influence selection. Several statistical methods have been developed recently for this purpose. Here, we present results an individual‐based simulation study investigating power and error rate popular or scan methods: linear regression, Bayescan, BayEnv LFMM. Contrary previous studies, focus on complex, hierarchical population...
Summary Genome‐scan methods are used for screening genomewide patterns of DNA polymorphism to detect signatures positive selection. There two main types methods: (i) ‘outlier’ detection based on that loci with high differentiation compared the rest genome and (ii) environmental association test between allele frequencies variables. We present a new ‐based genome‐scan method, BayeScEnv, which incorporates information in form ‘environmental differentiation’. It is F model, but, as opposed...
Abstract Population genetics is transitioning into a data-driven discipline thanks to the availability of large-scale genomic data and need study increasingly complex evolutionary scenarios. With likelihood Bayesian approaches becoming either intractable or computationally unfeasible, machine learning, in particular deep algorithms are emerging as popular techniques for population genetic inferences. These rely on that learn non-linear relationships between input model parameters being...
Abstract We compare the performance of Nm estimates based on F ST and R obtained from microsatellite data using simulations stepwise mutation model with range constraints in allele size classes. The results suggest that use loci can lead to serious overestimations , particularly when population sizes are large ( N > 5000) high K < 20). also indicate that, small ≤ 500) migration rates moderate ≈ 2), violations assumption used derive estimators biased results. Under ideal conditions,...
The spatial structuring of intraspecific genetic diversity is the result random drift, natural selection, migration, mutation, and their interaction with historical processes. contribution each has been typically difficult to estimate, but recent advances in statistical genetics have provided valuable new investigative tools tackle such complexity. Using a combination methods, we examined roles environment (i.e., selection), processes drift), demography life histories (e.g., feeding...
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) particular, are flawed a number of ways, therefore inappropriate for analysis phylogeographic data. These further argue Nested Clade Phylogeographic Analysis (NCPA) offers best approach statistical phylogeography. In order to remove confusion misconceptions introduced by these papers, we justify explain reasoning behind inference. We ABC is statistically valid...
Abstract We present a new multilocus genotype method that makes inferences about recent immigration rates and identifies the environmental factors are more likely to explain observed gene flow patterns. It also estimates population-specific inbreeding coefficients, allele frequencies, local population FST's performs individual assignments. generate synthetic data sets determine region of parameter space where our is not able provide accurate estimates. Our simulation study indicates reliable...
We compare the two main classes of measures population structure in genetics: (i) fixation such as FST,GST, and θ (ii) allelic differentiation Jost's D entropy differentiation. These groups quantify complementary aspects structure, which have no necessary relationship with each other. focus especially on empirical relevant to conservation analyses. At level, first set nearness fixation, while second relative degree The sets do not compete Fixation are often misinterpreted applications; we...
What shapes variation in genetic structure within a community of codistributed species is central but difficult question for the field population genetics. With focus on isolated coral reef ecosystem Hawaiian Archipelago, we assessed how life history traits influence 35 animals. Despite archipelago's stepping stone configuration, isolation by distance was least common type structure, detected four species. Regional structuring (i.e. division sites into genetically and spatially distinct...
Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue this regard, relates architecture underlying fitness traits. Theory predicts that may involve many...
Biological diversity is a key concept in the life sciences and plays fundamental role many ecological evolutionary processes. Although biodiversity inherently hierarchical covering different levels of organization (genes, population, species, communities ecosystems), index that behaves consistently across these has so far been lacking, hindering development truly integrative studies. To fill this important knowledge gap, we present unifying framework for measurement organization. Our...