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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Genetic evaluation of population structure in white marlin (Kajikia albida): the importance of statistical power
TL;DR: Genetic evaluation of population structure in white marlin (Kajikia albida): the importance of statistical power Nadya R. Mamoozadeh*, Jan R. McDowell, Jay R. Rooker, and John E. Graves report.
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Current genetic admixture between relictual populations might enhance the recovery of an elusive carnivore
Lise-Marie Pigneur,Gaëlle Caublot,Christine Fournier-Chambrillon,Pascal Fournier,Gloria Giralda-Carrera,Xavier Gremillet,Bruno Le Roux,Daniel Marc,Franck Simonnet,Nathalie Smitz,Nathalie Smitz,Eric Sourp,Julien Steinmetz,Fermin Urra-Maya,Johan Michaux +14 more
TL;DR: It is revealed that otter populations seem to be split into five distinct groups, which resembles the genetic pattern noted in many invasive exotic species derived from multiple sources and introduction events.
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Paths for colonization or exodus? New insights from the brown bear (Ursus arctos) population of the Cantabrian Mountains.
TL;DR: The results reveal the presence of two different mitochondrial (matrilineal) haplotypes in the Cantabrian population, both belonging to European brown bear clade 1a, and show that CanE is closer to the historical Pyrenean (Pyr) haplotype than to CanW.
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Bighorn Sheep Genetic Structure in Wyoming Reflects Geography and Management
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Conservation genetics of two critically endangered island dwarf carnivores
TL;DR: The authors' mitochondrial results support that both Cozumel carnivores are divergent from continental populations, strengthening their endemic status and discussing specific conservation measures that should include genetic information, directed to the long-term viability of these endemic carnivores.
References
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