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
Combining landscape genetics, radio-tracking and long-term monitoring to derive management implications for Natterjack toads (Epidalea calamita) in agricultural landscapes
Manuel Frei,Daniela Csencsics,Sabine Brodbeck,Esther Schweizer,Christoph Bühler,Felix Gugerli,Janine Bolliger +6 more
TL;DR: It is concluded that the Natterjack toad is well established in the intensely managed agricultural landscape, given that (i) large populations are maintained which may act as sources to spatially distributed occurrences, and (ii) the intensively managed landscape is sufficiently interspersed with suitable breeding habitats.
Journal ArticleDOI
Population substructure and signals of divergent adaptive selection despite admixture in the sponge Dendrilla antarctica from shallow waters surrounding the Antarctic Peninsula.
Carlos Leiva,Carlos Leiva,Sergi Taboada,Sergi Taboada,Nathan J. Kenny,David J. Combosch,Gonzalo Giribet,Thibaut Jombart,Ana Riesgo +8 more
TL;DR: The study unveils an unexpectedly long‐distance larval dispersal exceptional in Porifera, broadening the use of genome‐wide markers within nonmodel Antarctic organisms.
Journal ArticleDOI
Using genomics to design and evaluate the performance of underwater forest restoration
Georgina Wood,Ezequiel M. Marzinelli,Ezequiel M. Marzinelli,Adriana Vergés,Alexandra H. Campbell,Peter D. Steinberg,Melinda A. Coleman +6 more
Journal ArticleDOI
Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla
Nathan V. Whelan,Nathan V. Whelan,Matthew P. Galaska,Breanna N. Sipley,Jennifer M. Weber,Paul D. Johnson,Kenneth M. Halanych,Brian S. Helms +7 more
TL;DR: It is shown that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream‐biased, conflicting with previous hypotheses, and genetic diversity was highest in downstream populations.
Journal ArticleDOI
Sex ratio and gamete size across eastern North America in Dictyostelium discoideum, a social amoeba with three sexes.
TL;DR: Overall, the data are consistent with balancing selection acting on D. discoideum mating types, but with a sufficiently weak rare sex advantage to allow for drift, a potential explanation for why these amoebae have only three mating types.
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