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
Processes and drivers of Prosopis invasions in Eastern Africa
TL;DR: The lack of genetic differentiation between some species from the native range supports the notion that hybridization between allopatric species may occur frequently when they are cointroduced into new ranges.
Journal ArticleDOI
Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources
Mare Geraerts,Carl Vangestel,Tom Artois,Jorge M.O. Fernandes,Michiel Wp Jorissen,Auguste Chocha Manda,Célestin Danadu Mizani,Karen Smeets,Jos Snoeks,Gontran Sonet,Tingbao Yang,Maarten Van Steenberge,Emmanuel Vreven,Soleil Lunkayilakio Wamuini,Maarten P.M. Vanhove,Tine Huyse +15 more
TL;DR: It is concluded that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness.
Journal ArticleDOI
Past climatic refugia and landscape resistance explain spatial genetic structure in Oriental beech in the South Caucasus
Katarzyna Sękiewicz,Irina Danelia,Vahid Farzaliyev,Hamid Gholizadeh,Grzegorz Iszkuło,Alireza Naqinezhad,Elias Ramezani,Peter Thomas,Dominik Tomaszewski,Łukasz Walas,Monika Dering +10 more
TL;DR: In this article , the authors investigated processes that shaped the neutral genetic structure of Oriental beech (Fagus orientalis), aiming to assess the potential risks involved due to possible future distribution changes in the species.
Journal ArticleDOI
Population genomic insights into invasion success in a polyphagous agricultural pest, Halyomorpha halys
TL;DR:
Journal ArticleDOI
Population genetic structure in a rapidly expanding mesocarnivore: golden jackals in the Dinaric-Pannonian region
Astrid Vik Stronen,Marjeta Konec,Barbara Boljte,Ivica Bošković,Dragan Gačić,Ana Galov,Miklós Heltai,Maja Jelenčič,Franc Kljun,Ivan Kos,Tamara Kovačič,József Lanszki,Krunoslav Pintur,Boštjan Pokorny,Tomaž Skrbinšek,Franz Suchentrunk,László Szabó,Nikica Šprem,Kristijan Tomljanović,Hubert Potočnik +19 more
TL;DR: In this paper, the authors predicted similar ancestry for Slovenian jackals, and examined samples from Croatia, including Dalmatia and interior regions, Serbia, Hungary, and Slovenia with 25 microsatellite markers to determine population genetic structure.
References
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