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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An integrated framework to identify wildlife populations under threat from climate change
Orly Razgour,Orly Razgour,Orly Razgour,John B. Taggart,Stéphanie Manel,Javier Juste,Carlos F. Ibáñez,Hugo Rebelo,Hugo Rebelo,Antton Alberdi,Gareth Jones,Kirsty J. Park +11 more
TL;DR: An applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential is proposed and can be applied to vertebrates with limited dispersal abilities.
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Biogeography of Paenibacillus larvae, the causative agent of American foulbrood, using a new multilocus sequence typing scheme
Barbara Joy Morrissey,Barbara Joy Morrissey,Thorunn Helgason,Lena Poppinga,Anne Fünfhaus,Elke Genersch,Giles E. Budge +6 more
TL;DR: The first multilocus sequence typing scheme (MLST) for P. larvae is created, which largely confirms the previous enterobacterial repetitive intergenic consensus (ERIC)–polymerase chain reaction (PCR)-based typing scheme's divisions while providing added resolution and improved repeatability.
Journal ArticleDOI
Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader.
Daniel Selechnik,Mark F. Richardson,Richard Shine,Jayna L. DeVore,Simon Ducatez,Lee A. Rollins +5 more
TL;DR: It is found that toads form three genetic clusters: 1) native range toads, 2) toads from the source population in Hawaii and long-established areas near introduction sites in Australia, and 3) toad from more recently established northern Australian sites.
Journal ArticleDOI
Multiple-Geographic-Scale Genetic Structure of Two Mangrove Tree Species: The Roles of Mating System, Hybridization, Limited Dispersal and Extrinsic Factors
TL;DR: The first evidence of ongoing hybridization between Avicennia species and that these hybrids are fertile is reported, although this interspecific crossing has not contributed to an increase in the genetic diversity the populations where A. germinans and A. schaueriana hybridize.
Journal ArticleDOI
Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates.
Hernán E. Morales,Alexandra Pavlova,Nevil Amos,Nevil Amos,Richard E. Major,Andrzej Kilian,Chris Greening,Paul Sunnucks +7 more
TL;DR: A genomic cluster of differentiation and signatures of selection in a region with an over-representation of nuclear genes that interact with mitochondrial genes in a songbird is found, consistent with mitonuclear co-evolution as an important mechanism for population divergence and local adaptation.
References
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