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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The influence of environmental variation on the genetic structure of a poison frog distributed across continuous Amazonian rainforest
TL;DR: It is shown that significant phylogenetic divergence in the absence of obvious biogeographical barriers is shown and that finer-scaled measures of genetic structure show patterns that are associated with environmental variables also known to predict the density of A. femoralis.
Journal ArticleDOI
Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island.
Joshua M. Miller,Maud C. Quinzin,Elizabeth H Scheibe,Claudio Ciofi,Fredy Villalva,Washington Tapia,Adalgisa Caccone +6 more
TL;DR: Genetic pedigree analyses are used to examine 3 seasons of a pilot breeding program for the Floreana island Galapagos giant tortoise, C. niger, that had been declared extinct for ~150 years until individuals with mixed ancestry were recently discovered.
Journal ArticleDOI
Identification of Quantitative Trait Loci for Altitude Adaptation of Tree Leaf Shape With Populus szechuanica in the Qinghai-Tibetan Plateau.
Meixia Ye,Xuli Zhu,Xuli Zhu,Pan Gao,Pan Gao,Libo Jiang,Libo Jiang,Rongling Wu,Rongling Wu,Rongling Wu +9 more
TL;DR: To reveal how plants alter ecological adaptation to altitude through genes, Populus szechuanica var.
Journal ArticleDOI
Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip.
V. R. Kharzinova,Arsen V Dotsev,T.E. Deniskova,A. D. Solovieva,V. I. Fedorov,K. A. Layshev,Tatiana M Romanenko,I. M. Okhlopkov,Klaus Wimmers,Henry Reyer,Gottfried Brem,Natalia A Zinovieva +11 more
TL;DR: This study revealed a clear genetic differentiation between domestic and wild reindeer populations, and provides novel insights into the genetic diversity and structure of reindeers populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species.
Journal ArticleDOI
A mountain range is a strong genetic barrier between populations of Afzelia quanzensis (pod mahogany) with low genetic diversity
TL;DR: The relatively low level of genetic diversity in Afzelia quanzensis may reduce adaptability and limit future evolutionary responses, and genetic resource management should take into consideration the existence of the distinct gene pools to capture the entire extant genetic variation.
References
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