DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors
TLDR
A new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ' , χ2 test for population heterogeneity), among others.Abstract:
Summary
We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ', χ2 test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective.
diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs).
Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis.read more
Citations
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Journal ArticleDOI
Population genetic structure of the bank vole Myodes glareolus within its glacial refugium in peninsular Italy
Andrea Chiocchio,Paolo Colangelo,Gaetano Aloise,Giovanni Amori,Giovanni Amori,Sandro Bertolino,Roberta Bisconti,Riccardo Castiglia,Daniele Canestrelli +8 more
TL;DR: The authors investigated the patterns of genetic variation in the bank vole Myodes glareolus within the Italian peninsula and found more intra-specific variation than expected based on previous assessments, supporting a scenario whereby the high levels of intraspecific diversity observed within major glacial refugia are better explained by dynamic micro-evolutionary processes occurred within these areas, rather than by longterm demographic stability of refugial population.
Journal ArticleDOI
Founder effects determine the genetic structure of the water flea Daphnia in Ethiopian reservoirs
Tsegazeabe Hadush Haileselasie,Tsegazeabe Hadush Haileselasie,Joachim Mergeay,Joost Vanoverbeke,Luisa Orsini,Luc De Meester +5 more
TL;DR: The results show that rapid colonization of empty habitats and fast population growth by a handful of founders can result in strong founder effects, even in relatively large habitats that are likely regularly reached by new immigrants.
Journal ArticleDOI
An approach for identifying cryptic barriers to gene flow that limit species' geographic ranges.
TL;DR: Habitat variables that constrain gene flow across the entire geographic range of an endemic salamander in the eastern United States are identified, and whether increased resistance resulting from these variables provides cryptic dispersal barriers at the range edges is tested.
Dissertation
Large-scale releases of native species: the mallard as a predictive model system
TL;DR: A significant difference between wild and farmed mallards concerning longevity, migration, bill morphology and genetic structure was also found, together with signs of cryptic introgression of farmed genotypes in the wild population with potential fitness reduction as a result.
Journal ArticleDOI
The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye (Sander vitreus).
TL;DR: This study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
References
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