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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Posted ContentDOI
Small in-stream barriers contribute little to strong local population genetic structure in five hololimnic macroinvertebrate taxa
TL;DR: Comparing population genomic analysis and population genomic simulations shows that the actual population structure deviated from initial expectations for the five macroinvertebrate species, and that individual small in-stream barriers do not contribute substantially to the strong population differentiation.
Journal ArticleDOI
Genetic Melting Pot in Blacklegged Ticks at the Northern Edge of their Expansion Front.
TL;DR: This study investigated genetic connectivity and differentiation in blacklegged ticks, in an area of putatively recent advance in Ontario and Quebec, Canada, using microsatellite markers, suggesting patchy differentiation of alleles, no spatial pattern of genetic structure, and genetic subdivision within sites, which are consistent with the very limited evidence available near the leading edge of range expansion ofblacklegged ticks into Canada.
Journal ArticleDOI
Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns.
Aaliyah D. Wright,Nicole L. Garrison,Nicole L. Garrison,Ashantye' S Williams,Paul D. Johnson,Nathan V. Whelan,Nathan V. Whelan +6 more
TL;DR: The results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.
Journal ArticleDOI
Population structure of North Pacific gray whales in light of trans-Pacific movements
Aimee R. Lang,David W. Weller,Alexander M. Burdin,Kelly M. Robertson,Olga Sychenko,R Jorge Urbán,Sergio Martínez-Aguilar,Victoria L. Pease,Richard G. LeDuc,D. I. Litovka,Vladimir N. Burkanov,Vladimir N. Burkanov,Robert L. Brownell +12 more
Journal ArticleDOI
No leading‐edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications
Yacine Ben Chehida,Roisin Loughnane,Julie Thumloup,Kristin Kaschner,Cristina Garilao,Patricia E. Rosel,Michael C. Fontaine,Michael C. Fontaine +7 more
TL;DR: The authors used phylogenetics, population genetics, and predictive habitat modeling to investigate population structure and phylogeographic history of the North Atlantic porpoises, and found that porpoise populations from both sides of North Atlantic form a continuous system belonging to the same subspecies.
References
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