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
An integrative study of species distribution modelling and conservation genetics: Magnolia in Hispaniola
Tim Claerhout,Diederik Strubbe,Ramón Castillo Torres,Marie-Stéphanie Samain,Lars W. Chatrou,Emily Veltjen +5 more
TL;DR: In this article , the potential distribution and the genetic health of the Magnolias of Hispaniola were assessed using species distribution modeling (SDM) to predict habitat suitability for the Magnolia of Hispania by analysing 21 variables, describing climate and landscape features, on 635 occurrences.
Journal ArticleDOI
Population genetics of a lethally managed medium‐sized predator
TL;DR: In this article , the authors investigated genetic structure, variation and relatedness of 178 culled jackals on private small-livestock farms in the central Karoo of South Africa using 13 microsatellites.
Journal ArticleDOI
The blowfly Chrysomya latifrons inhabits fragmented rainforests, but shows no population structure
Nathan J. Butterworth,James F. Wallman,Nikolas P. Johnston,Blake M. Dawson,Joshua Sharp-Heward,Angela McGaughran +5 more
TL;DR: In this article , the authors genotyped 188 blowflies ( Chrysomya latifrons ) from 15 isolated rainforests and found high levels of gene flow, a lack of genetic structure between rain forests, and low genetic diversity, suggesting the presence of a single large genetically depauperate population.
Dissertation
Caractérisation de la diversité du répertoire TCR par modélisation de données de séquençage haut-débit
TL;DR: Dans ce contexte, les objectifs de ma these ont ete de approfondir le concept de diversite du repertoire lymphocytaire, mettre au point une methodologie adaptee permettant d'exploiter les donnees de sequencage de maniere optimale en prenant en compte les limites of cette technologie.
Journal ArticleDOI
Geographical context outweighs habitat disturbance effects in explaining mistletoe population genetic differentiation at a regional scale
Francisco E. Fontúrbel,Gloria B. Rodríguez-Gómez,José I. Orellana,Jorge Cortés-Miranda,Noemi Rojas-Hernandez,Caren Vega-Retter +5 more
TL;DR: The results suggest that mistletoe genetic differentiation at a regional scale was more influenced by historical events than to habitat disturbance, and habitat disturbance can indirectly affect Mistletoe population genetic differentiation via the seed dispersal process, which may increase inbreeding levels.
References
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