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
Human-driven genetic differentiation in a managed red deer population
TL;DR: Efforts to sustainably preserve the genetic diversity of the entire region should focus on measures ensuring genetic connectivity, as opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.
Posted ContentDOI
Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator
Germain Boussarie,Germain Boussarie,Paolo Momigliano,William D. Robbins,Lucas Bonnin,Lucas Bonnin,Jean-François Cornu,Cécile Fauvelot,Cécile Fauvelot,Jeremy J. Kiszka,Stéphanie Manel,David Mouillot,Laurent Vigliola +12 more
TL;DR: In this article, a seascape genomic approach based on isolation-by-resistance models involving circuit theory was applied to 515 shark samples, genotyped for 4,491 nuclear single-nucleotide polymorphisms, to explore which parameters drive their population genetic differentiation.
Journal ArticleDOI
Advanced software programs for the analysis of genetic diversity in livestock genomics: a mini review
TL;DR: The use of high throughput molecular marker technologies, advanced statistical and software tools have revolutionized the precision of animal genetic diversity analysis in a large number of populations with limited time and resources.
Journal ArticleDOI
Genetic drift precluded adaptation of an insect seed predator to a novel host plant in a long-term selection experiment.
TL;DR: The results suggest that this insect herbivore is not likely to adapt to a novel host species in a time-scale of 20 generations despite sufficient genetic variation and that genetic drift disrupted the response to selection.
Journal ArticleDOI
The role of the Strait of Gibraltar in shaping the genetic structure of the Mediterranean Grenadier, Coryphaenoides mediterraneus, between the Atlantic and Mediterranean Sea
Diana Catarino,Sergio Stefanni,Per Erik Jorde,Gui M. Menezes,Francis Neat,Halvor Knutsen,Halvor Knutsen +6 more
TL;DR: Very limited genetic exchange is suggested between Atlantic and Mediterranean populations of C. mediterraneus, likely due to the shallow bathymetry of the Strait of Gibraltar acting as a barrier to gene flow.
References
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