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
Multi-method approach to advance provenance determination of fish in stocked systems
Susannah M. Leahy,Dean R. Jerry,B.B. Wedding,Julie B. Robins,T.C. Wright,Aleksey Sadekov,David B. Jones,Samuel M. Williams,S. Grauf,Mark McLennan,Michelle J. Sellin,Julie Goldsbury,Richard J. Saunders +12 more
TL;DR: In this article , a case study of barramundi (Lates calcarifer) in the Dry Tropics region of northern Australia was used for provenance determination using Near Infra-Red Spectroscopy (NIRS).
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Applying novel connectivity networks to wood turtle populations to provide comprehensive conservation management strategies for species at risk
TL;DR: In this article , the authors used graph theory to evaluate populations for conservation purpose without focusing solely on individual nodes, and proposed a BRIDES selection process to assist conservation biologists in the prioritization of populations, and compared BRIDES results and assess gene flow among wood turtle populations.
Journal ArticleDOI
Genetic diversity and grouping of pigeonpea [Cajanus cajan Millspaugh] Germplasm using SNP markers and agronomic traits
TL;DR: In this article , the authors assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits.
Journal ArticleDOI
Identification of Sable (Martes zibellina L.) Populations in the Southern Part of the Species Range
S. N. Kashtanov,M. V. Shitova,M. M. Somova,P. A. Filimonov,O. Yu. Tyutenkov,A. A. Khodireva,Gulnara R. Svishcheva,I. G. Meshchersky,Yu. A. Stolpovsky,Viatcheslav V. Rozhnov +9 more
TL;DR: In this article, a panel of 15 microsatellite loci was used to study the modern structure of the sable gene pool in the southern part of the range and a high level of population differentiation was determined.
Journal ArticleDOI
Trait evolution during a rapid global weed invasion despite little genetic differentiation
Ramona-Elena Irimia,Daniel Montesinos,A.K. Chaturvedi,Ian R. Sanders,Jose Luis Hierro,Gastón J. Sotes,Lohengrin A. Cavieres,Özkan Eren,Christopher J. Lortie,Kris French,Adrian C. Brennan +10 more
TL;DR: In this paper , the authors explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (FST), and comparing it with PST in a common garden experiment in individuals originating from regions representing the species distribution across five continents.
References
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