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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A trait-based approach to predict population genetic structure in bees.
TL;DR: The results suggest that physical dispersal or other functions related to body size are among the most critical for mediating population structure for bees, and the importance of standardizing population genetic measures to more easily compare studies and to identify the most susceptible species to landscape and climatic changes.
Journal ArticleDOI
Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds.
Alexander A Sermyagin,Arsen V Dotsev,E. A. Gladyr,A. Traspov,T.E. Deniskova,O. V. Kostyunina,Henry Reyer,Klaus Wimmers,Mario Barbato,Ivan A. Paronyan,K. V. Plemyashov,Johann Sölkner,Ruslan Popov,Gottfried Brem,Natalia A Zinovieva +14 more
TL;DR: Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle.
Journal ArticleDOI
Do plant populations on distinct inselbergs talk to each other? A case study of genetic connectivity of a bromeliad species in an Ocbil landscape.
Karina Vanessa Hmeljevski,Alison G. Nazareno,Marcelo Leandro Bueno,Maurício Sedrez dos Reis,Rafaela Campostrini Forzza +4 more
TL;DR: Genetic analyses highlighted the low genetic connectivity and long‐term persistence of populations, and the founder effect and genetic drift seemed to have been very important processes that shaped the current diversity and genetic structure observed in both genomes.
Journal ArticleDOI
Ecological and evolutionary consequences of alternative sex-change pathways in fish
TL;DR: It is observed that, regardless of the direction of sex change, individuals conform to the same overall strategy, producing more offspring and exhibiting greater Vk* in the second sex, however, protogynous species show greater VK*,, resulting in an overall reduction of Ne compared to protandrous species.
Journal ArticleDOI
Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.
TL;DR: Spatial genetic analysis of the economically important European lobster revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea.
References
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