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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Dissertation
Population status and genetic diversity of the endemic black-billed gull Larus bulleri of New Zealand
TL;DR: The history and formation of braided rivers in New Zealand, and the challenges of historical black-billed gull counts, are described.
Journal ArticleDOI
Genetic structure and the history of chub in the Alvord Basin
Christian T. Smith,Jennifer Von Bargen,Patrick W. DeHaan,Paul D. Scheerer,Michael H. Meeuwig +4 more
TL;DR: The results revealed that diversity in Alvord Chub was primarily distributed among two regional groupings, which the authors hypothesize to be related to habitat changes following the end of the most recent glaciation event, approximately 10 thousand years ago.
ReportDOI
Ontwikkeling van een monitoringsprotocol voor heikikker: Bepaling van de aanwezigheid en verhouding bruine en heikikker via (e)DNA-barcoding en opstart genetische monitoring
Journal ArticleDOI
Tabula rasa in the Patagonian Channels II: The cushion peat bog species Astelia pumila (Asteliaceae) and Donatia fascicularis (Stylidiaceae) survived the last glacial in south‐central Chile
Simon Pfanzelt,Simon Pfanzelt,Petra Šarhanová,Petra Šarhanová,Dirk C. Albach,K. Bernhard von Hagen +5 more
TL;DR: A broader picture is provided of how West Patagonian moorland plants responded to the Quaternary ice‐ages to test the hypothesis of a glacial refugium for moor land plants in south‐central Chile and the tabula rasa scenario for the Patagonia Channels.
References
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