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
Changes in barley (Hordeum vulgare L. subsp. vulgare) genetic diversity and structure in Jordan over a period of 31 years
I. Thormann,Patrick A. Reeves,S. Thumm,Ann Reilley,Johannes M.M. Engels,Chandrashekhar Biradar,Ulrike Lohwasser,Andreas Börner,Klaus Pillen,Christopher M. Richards +9 more
TL;DR: While the amount of genetic diversity in terms of allelic richness and number of multi-locus genotypes has been maintained, local distinctiveness among landrace barley populations in Jordan was reduced.
Journal ArticleDOI
Signatures of adaptive divergence among populations of an avian species of conservation concern.
TL;DR: The results provide a first look at local adaption for isolated populations of a single species and suggest adaptive divergence in multiple metabolic and biochemical pathways may be occurring.
Journal ArticleDOI
Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs
TL;DR: It is attests that EST‐SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.
Journal ArticleDOI
New microsatellite loci for annatto ( Bixa orellana ), a source of natural dyes from Brazilian Amazonia
Gabriel Dequigiovanni,Santiago Linorio Ferreyra Ramos,Maria Teresa Gomes Lopes,Charles R. Clement,Doriane Picanço Rodrigues,Eliane Gomes Fabri,Maria Imaculada Zucchi,Elizabeth Ann Veasey +7 more
TL;DR: Higher genetic diversity estimates were detected for the wild populations when compared to the cultivated populations, and higher apparent outcrossing rates were found for the two wild than the cultivated population, which indicate a mixed mating system for the species.
Posted ContentDOI
Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (Oncorhynchus nerka)
TL;DR: The SNPs and genomic regions identified in this study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
References
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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.
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