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
Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region.
TL;DR: In this article, population genetic and outlier detection analyses were performed using 10,593 genome-wide single nucleotide polymorphisms (SNPs) from 16 geographically disparate Indo-Pacific P. monodon populations.
Journal ArticleDOI
New genetic evidences for distinct populations of the common minke whale (Balaenoptera acutorostrata) in the Southern Hemisphere
Lucas Milmann,Mioko Taguchi,Salvatore Siciliano,Julio Baumgarten,Larissa Rosa de Oliveira,Victor Hugo Valiati,Mutsuo Goto,Paulo Henrique Ott,Luis A. Pastene +8 more
TL;DR: Results suggested that the taxonomical status of common minke whales in the Southern Hemisphere should be revised and that regardless of their taxonomic status, dwarf common minkel whales from WSA and WSP are unique populations that require separate management for conservation.
Posted ContentDOI
Parallel use of a shared genomic island of speciation in clinal and mosaic hybrid zones between cryptic seahorse lineages
Florentine Riquet,Cathy Liautard-Haag,Lucy C. Woodall,Carmen Bouza,Patrick Louisy,Bojan Hamer,Francisco Otero-Ferrer,Philippe Aublanc,Vickie Beduneau,Olivier Briard,Tahani El Ayari,Sandra Hochscheid,Khalid Belkhir,Sophie Arnaud-Haond,Pierre-Alexandre Gagnaire,Nicolas Bierne +15 more
TL;DR: It is reported that the low diversity long-snouted seahorse Hippocampus guttulatus is genetically subdivided into five cryptic semi-isolated lineages, and how a genomic hotspot of parallel differentiation could have evolved and become associated either with space or with a patchy environment in a single study system is discussed.
Dissertation
Molecular phylogeny and seascape genetics of the panulirus homarus subspecies in the Western Indian Ocean.
TL;DR: In this article, the authors used maximum likelihood and Bayesian inference to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific and found that P. h. rubellus from the southwest Indian Ocean is a separately evolving lineage and possibly a separate species.
Dissertation
The ecology and conservation of the Adonis Blue (Polyommatus bellargus) and the Chalkhill Blue (Polyommatus coridon) butterflies in the UK
TL;DR: This thesis examines and compares the ecology of two closely butterfly species, polyommatus bellargus and Polyommatus coridon in southern England; calcareous grassland specialists, found in a highly fragmented ecosystem at the northern most edge of their geographic range.
References
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