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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Influences of multilocus heterozygosity on size during early life
TL;DR: Analysis of patterns in population and individual genetic diversity and the effect of genetic diversity on individual fitness among life stages and populations of captive yellow perch stocked into two ponds indicates that the influence of heterozygosity may be mediated through an interaction, likely viability selection, between ontogeny and environment that is most important during early life.
Journal ArticleDOI
The origin and population genetics of wolves in the north Hungarian mountains
Péter Fehér,Krisztián Frank,Péter Gombkötő,Robin Rigg,Péter Bedő,Dóra Újváry,Viktor Stéger,László Szemethy +7 more
TL;DR: In this article , Hungarian wolf samples were also analyzed using kinship methods and found that there is ongoing gene flow across the Slovakian-Hungarian border, and no evidence that individuals originating in captivity have played any role in the recolonisation process.
Journal ArticleDOI
Role of drainage and barriers in the genetic structuring of a tessellated darter population
TL;DR: It is found that healthy populations of darters may naturally be structured by drainage, but likely disperse across barriers enough to retain drainage-wide homogeneity.
Journal ArticleDOI
Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change
TL;DR: In this paper , the authors used outlier scans and genetic-environment association analyses to identify genomic variation putatively underlying local adaptation across the species' geographic range and found evidence for adaptation with a polygenic architecture and a set of candidate SNPs that identify genes putatively contributing to local adaptation.
Journal ArticleDOI
Genomic population structure of Parkia platycephala Benth. (Leguminosae) from Northeastern Brazil
João Gabriel Silva Morais,Marcones Ferreira Costa,Alessandro Alves-Pereira,Maria Imaculada Zucchi,José Baldin Pinheiro,Ademir Sérgio Ferreira de Araújo,Verônica Brito DA Silva,Regina Lucia Ferreira-Gomes,Ângela Celis de Almeida Lopes +8 more
References
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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).
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GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism
Michel Raymond,François Rousset +1 more
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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.
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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.
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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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