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
More filters
Journal ArticleDOI
The effects of a motorway on movement behaviour and gene flow in a forest carnivore: Joint evidence from road mortality, radio tracking and genetics
Filipe Carvalho,André Lourenço,Rafael Carvalho,Paulo C. Alves,Paulo C. Alves,António Mira,Pedro Beja,Pedro Beja +7 more
TL;DR: This paper examined the individual-and population-level barrier effects of a motorway on the common genet Genetta genetta, by combining long-term road mortality, radio tracking and population genetics data.
Journal ArticleDOI
Convergent adaptation to dangerous prey proceeds through the same first‐step mutation in the garter snake Thamnophis sirtalis
TL;DR: Convergence in the evolution of channel resistance is likely the result of shared biases in the two lineages of T. sirtalis—only a few mutational routes can confer TTX resistance while maintaining the conserved function of voltage‐gated sodium channels.
Journal ArticleDOI
Cryptic Plutella species show deep divergence despite the capacity to hybridize.
K. D. Perry,K. D. Perry,Gregory J. Baker,Kevin J. Powis,Joanne K. Kent,Christopher M. Ward,Simon W. Baxter +6 more
TL;DR: Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact.
Journal ArticleDOI
Contrasting gene flow at different spatial scales revealed by genotyping-by-sequencing in Isocladus armatus, a massively colour polymorphic New Zealand marine isopod.
Sarah J. Wells,James Dale +1 more
TL;DR: This study provides one of the first population genomic studies of a marine organism in New Zealand, and suggests that genotyping-by-sequencing can be a good alternative to more traditional investigations based on traditional markers such as microsatellites.
Journal ArticleDOI
Regional genetic structure of sandfish Holothuria (Metriatyla) scabra populations across the Philippine archipelago
TL;DR: Examination of genetic diversity and spatial patterns of genetic structure of sandfish populations across the Philippine archipelago revealed weak yet significant regional genetic structure among 15 H. scabra populations.
References
More filters
Journal ArticleDOI
Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
TL;DR: The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973).
Journal ArticleDOI
GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism
Michel Raymond,François Rousset +1 more
Journal ArticleDOI
G(ST) and its relatives do not measure differentiation.
TL;DR: G ST and its relatives are often interpreted as measures of differentiation between subpopulations, with values near zero supposedly indicating low differentiation, but GST necessarily approaches zero when gene diversity is high, and it is not monotonic with increasing differentiation.
Journal ArticleDOI
A practical solution to the pervasive problems of p values.
TL;DR: The BIC provides an approximation to a Bayesian hypothesis test, does not require the specification of priors, and can be easily calculated from SPSS output.
Journal ArticleDOI
genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms
TL;DR: Two programs, GENOTYPE and GENODIVE, developed for analyses of clonal diversity in asexually reproducing organisms, show that genotype can be used for detecting genotyping errors in studies of sexual organisms.
Related Papers (5)
Inference of population structure using multilocus genotype data
Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
Dent Earl,Bridgett M. vonHoldt +1 more