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
Gene flow and effective population sizes of the butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape
An Vanden Broeck,Dirk Maes,Andreas Kelager,Irma Wynhoff,Michiel F. WallisDeVries,Michiel F. WallisDeVries,David R. Nash,J. Gerard B. Oostermeijer,Hans Van Dyck,Joachim Mergeay +9 more
TL;DR: In this article, the authors assess contemporary interpopulation connectedness of the threatened myrmecophilous butterfly, Maculinea alcon, in a highly fragmented landscape and infer dispersal, effective population sizes, genetic diversity and structure based on 14 locations of M. alcon in Belgium and the Netherlands using data from 12 microsatellite loci.
Journal ArticleDOI
Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka).
TL;DR: The single nucleotide polymorphisms and genomic regions identified in this study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
Journal ArticleDOI
Decimated little brown bats show potential for adaptive change.
TL;DR: Evidence of selectively driven change (adaptation) is presented, despite dramatic nonadaptive genomic shifts (genetic drift) associated with population declines.
Journal ArticleDOI
Early genetic outcomes of American black bear reintroductions in the Central Appalachians, USA
Sean M. Murphy,John T. Hast,Ben C. Augustine,David W. Weisrock,Joseph D. Clark,David M. Kocka,Christopher W. Ryan,Jaime L. Sajecki,John J. Cox +8 more
TL;DR: For future bear reintroductions, it is suggested managers consider sourcing founders from populations with high genetic diversity and soft-releasing bears to locales that are, if possible, within the dispersal capability of extant populations to mitigate the potential consequences of founder effects and isolation.
Journal ArticleDOI
Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild
Catherine E. Grueber,Samantha Fox,Elspeth A. McLennan,Rebecca M. Gooley,David Pemberton,Carolyn J. Hogg,Katherine Belov +6 more
TL;DR: Examination of diversity of 31 putatively neutral and 11 MHC‐linked microsatellite loci of three remnant wild devil populations alongside computational diversity projections showed that populations had low diversity, connectivity was poor, and diversity has likely decreased over the last decade.
References
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