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
Rapid and repeatable host plant shifts drive reproductive isolation following a recent human-mediated introduction of the apple maggot fly, Rhagoletis pomonella.
Glen R. Hood,Thomas H. Q. Powell,Meredith M. Doellman,Sheina B. Sim,Mary M. Glover,Wee L. Yee,Robert B. Goughnour,Monte Mattsson,Dietmar Schwarz,Jeffrey L. Feder +9 more
TL;DR: The results suggest that conditions suitable for initiating host‐associated divergence may be common in nature, allowing for the rapid evolution of new host races when ecological opportunity arises.
Journal ArticleDOI
Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex
TL;DR: This study implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex and demonstrates the utility of model‐based approaches for phylogeographic inference.
Journal ArticleDOI
Reproductive philopatry in a coastal shark drives age-related population structure
Juliana D. Klein,Juliana D. Klein,Aletta E. Bester-van der Merwe,ML Dicken,Kolobe L. Mmonwa,Peter R. Teske +5 more
TL;DR: The results highlight the need to target young-of-the-year sharks when investigating reproductive philopatry to exclude roaming individuals that obscure size-related signals of genetic differentiation and recommend protected areas, or time-area closures, prohibiting exploitation in the nursery areas during pupping season.
Journal ArticleDOI
High Interannual Variability in Connectivity and Genetic Pool of a Temperate Clingfish Matches Oceanographic Transport Predictions.
Maria Klein,Sara Teixeira,Jorge Assis,Ester A. Serrão,Emanuel João Gonçalves,Rita Alexandra Borges,Rita Alexandra Borges +6 more
TL;DR: P measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations.
Journal ArticleDOI
The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative.
Josué Barrera-Redondo,Guillermo Sánchez-de la Vega,Jonás A. Aguirre-Liguori,Gabriela Castellanos-Morales,Yocelyn T. Gutiérrez-Guerrero,Xitlali Aguirre-Dugua,Erika Aguirre-Planter,Maud I. Tenaillon,Rafael Lira-Saade,Luis E. Eguiarte +9 more
TL;DR: In this article, Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh.
References
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