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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Elucidating the Clusia criuva species ‘complex’: cryptic taxa can exhibit great genetic and geographical variation
Maria Beatriz de Souza Cortez,Danilo Augusto Sforça,Fábio M. Alves,João de Deus Vidal,Alessandro Alves-Pereira,Gustavo Maruyama Mori,Gustavo Maruyama Mori,Isabela A.A. Andreotti,José E. do Nascimento,Volker Bittrich,Maria Imaculada Zucchi,Maria do Carmo Estanislau do Amaral,Anete Pereira de Souza +12 more
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Genomic inbreeding and population structure of northern pike ( Esox lucius ) in Xinjiang, China.
TL;DR: The results suggested that the extinction risk of northern pike was very low in Xinjiang of China, and the controlled capture fishery ofNorthern pike could be developed reasonably.
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Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls ( Larus bulleri)
Claudia Mischler,Andrew J. Veale,Tracey C. van Stijn,Rudiger Brauning,John C. McEwan,Richard F. Maloney,Bruce C. Robertson +6 more
TL;DR: It is inferred that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments, and the genetic structure of populations at the northern limit of the species’ range is investigated.
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Genetic signature of disease epizootic and reintroduction history in an endangered carnivore
TL;DR: The results suggest the importance of early and sustained management in mitigating disease epizootics in naïve populations for the maintenance of genetic diversity and the impacts of a novel pathogen on genetic diversity in a genetically depauperate endangered species.
References
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