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
When Invaders Go Unnoticed: The Case of Gracilaria vermiculophylla in the British Isles
Stacy A. Krueger-Hadfield,Stacy A. Krueger-Hadfield,Caroline L. Magill,Francis Bunker,Nova Mieszkowska,Erik E. Sotka,Christine A. Maggs +6 more
TL;DR: In this paper, the authors used a combination of morphological observations and 10 microsatellite loci to identify three populations of Gracilaria vermiculophylla in the British Isles and found that the populations at Carlingford Lough included both reproductive haploid gametophytes and diploid tetrasporophytes.
Journal ArticleDOI
Molecular genetic characterization and association mapping in spelt wheat
TL;DR: It is shown that there is no major population structure and no grouping according to the age of the accessions, in line with the short breeding history and the intensive use of old cultivars in the re-establishment of spelt.
Journal ArticleDOI
Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal.
Fabricio J. B. Francischini,Erick M. G. Cordeiro,Jaqueline Bueno de Campos,Alessandro Alves-Pereira,João Paulo Gomes Viana,Xing Wu,Wei Wei,Patrick J. Brown,Andrea L. Joyce,Gabriela Murua,Sofia Victoria Fogliata,Steven J. Clough,Steven J. Clough,Maria Imaculada Zucchi,Maria Imaculada Zucchi +14 more
TL;DR: The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas.
Journal ArticleDOI
Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing
James A. Kolmer,A. Herman,María E. Ordóñez,Silvia Germán,Alexey Morgounov,Z. A. Pretorius,B. Visser,Y. Anikster,Maricelis Acevedo +8 more
TL;DR: Isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the divergence of isolates found worldwide that are virulent to durum Wheat.
Journal ArticleDOI
Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species.
TL;DR: The findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species and may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.
References
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