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
Dissertation
Moving up: Using climate, physiology, and gene flow to characterize current and future geographic range limits in montane salamanders
TL;DR: Kozak et al. as mentioned in this paper presented an ecology, evolution, and behavior (E2B) approach to the problem of human-human interaction in the field of ecology, ecology, and biology.
Journal ArticleDOI
Connectivity patterns and gene flow among Chelon ramada populations
E. Pereira,C. S. Mateus,M. J. Alves,Rita Almeida,Joana Jordão Pereira,Bernardo R. Quintella,Pedro Almeida +6 more
TL;DR: In this article , the authors studied the genetic variation and infer patterns of gene flow and population connectivity along species' distribution across the Northeast Atlantic coast and the Mediterranean Sea, and found that the thinlip grey mullet display a high dispersal capability, that combined with continuous habitat availability and large population numbers, allow the maintenance of a unique genetic group.
Journal ArticleDOI
Invader at the edge — Genomic origins and physiological differences of round gobies across a steep urban salinity gradient
Leon Green,Ellika Faust,J. R. Hinchliffe,Jeroen Brijs,Andrew Holmes,Felix Englund Örn,Ola Svensson,Jonathan A. C. Roques,Erica H. Leder,Erik Sandblom,Charlotta Kvarnemo +10 more
TL;DR: In this paper , the authors used 12,937 SNPs to identify the genetic origin and diversity of three sites along the salinity gradient and round goby from western, central and northern Baltic Sea, as well as north European rivers.
Journal ArticleDOI
Genetic Diversity and Genome-Wide Association Study of Morphological and Quality Traits in Peach Using Two Spanish Peach Germplasm Collections
TL;DR: In this article , the SNP array was used to explore the genetic diversity and single nucleotide polymorphism (SNP)-trait associations in the Spanish germplasm, the new peach 18K SNP v2 array were used to genotype 287 accessions belonging to the two National Peach Germplasm Collections placed at the Agrifood Research and Technology Centre of Aragon (CITA) and at the Experimental Station of Aula Dei (EEAD)-CSIC.
Journal ArticleDOI
Baseline genetic distinctiveness supports structured populations of thornback ray in the Mediterranean Sea
Riccardo Melis,Laura Vacca,Alessia Cariani,Laura Carugati,Charis Charilaou,S. Di Crescenzo,Alice Ferrari,Maria Cristina Follesa,Cecilia Mancusi,Fabrizio Serena,Letizia Sion,Fausto Tinti,Rita Cannas +12 more
TL;DR: In this paper , microsatellite markers were used to unravel the genetic features (variability, connectivity, sex-biased dispersal) of R. clavata populations, both at the small (around the coast of Sardinia, western Mediterranean Sea) and larger spatial scales (at the pan-Mediterranean level, and between the Atlantic Ocean and the Mediterranean Sea).
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