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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Dissertation
Development and maintenance of genetic diversity in Scots pine, Pinus sylvestris (L.)
TL;DR: In this article, a multilevel approach was used to determine how different forces interact to shape and maintain within and among population genetic diversity of Scots pine and what the implications are for conservation and management under forthcoming environmental conditions.
Разработка мультиплексной панели микросателлитов для оценки достоверности происхождения и степени дифференциации популяций северного оленя Rangifer tarandus
В.Р. Харзинова,Е А Гладырь,В.И. Федоров,Т.М. Романенко,Л Д Шимит,К.А. Лайшев,Л А Калашникова,Н А Зиновьева +7 more
TL;DR: This paper is the first to present data on STR markers of reindeer of the Nenets breed from the Russian regional populations, the breeding zone of which almost completely covers the current range of the breed.
Expansion of the Sable (Martes zibellina L.) from the North of the Central Siberian Plateau into Tundra Ecosystems
S. N. Kashtanov,Eugeniy S. Zakharov,O. A. Begletsov,Gulnara R. Svishcheva,Serge Rychkov,Pavel Filimonov,A. A. Onokhov,E.S. Levenkova,I. G. Meschersky,Viatcheslav V. Rozhnov +9 more
Journal ArticleDOI
Species' attributes predict the relative magnitude of ecological and genetic recovery following mass mortality
TL;DR: In this paper , the authors couple ecological and genomic methods to test the hypothesis that species with attributes favouring greater dispersal potential (e.g., longer pelagic duration, higher fecundity and larger population size) have greater realized dispersal overall.
Journal ArticleDOI
Guiding marine protected area network design with comparative phylogeography and population genomics: An exemplary case from the Southern Ocean
Carlos Leiva,Ana Riesgo,David J. Combosch,María Belén Arias,Gonzalo Giribet,Rachel Downey,Nathan J. Kenny,Sergi Taboada +7 more
TL;DR: In this article , the authors use a multispecies and multilocus approach to provide recommendations for MPAn design, highlighting the importance of the species selected and the analyses performed.
References
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