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
Detecting mislabeling and identifying unique progeny in Acacia mapping population using SNP markers
Asif Javed Muhammad,Asif Javed Muhammad,Mohd Zaki Abdullah,Norwati Muhammad,R Wickneswari V Ratnam +4 more
TL;DR: Mislabeling seems to be a common problem due to the complexity involved in the production of mapping populations, therefore, checking for mislabeling is imperative for breeding activities and for analyses such as linkage mapping in which a correlation between genotypic and phenotypic data is determined.
Posted ContentDOI
Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes
TL;DR: This study used restriction site-associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric species in the Coregonus artedi complex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes.
Journal ArticleDOI
Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands.
Pamela Vega-Polo,María Mercedes Cobo,María Mercedes Cobo,Andrea Argudo,Bernardo Gutierrez,Bernardo Gutierrez,Jennifer K. Rowntree,María de Lourdes Torres +7 more
TL;DR: An extensive overview of the species across its distribution range in Ecuador is provided, contributing to a better understanding of its conservation status and can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.
Journal ArticleDOI
Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle.
Gulnara R. Svishcheva,Olga Babayan,Bulat Lkhasaranov,Ariuntuul Tsendsuren,Abdugani Abdurasulov,Yurii Stolpovsky +5 more
TL;DR: Using microsatellite data, various cattle breeds of European and Asian origins from different geo-climatic zones are analyzed to study their genetic diversity, genetic distances, population structure, and other characteristics, finding that the Altai cattle is genetically close to the Kyrgyz one.
Journal ArticleDOI
Paternity analysis, pollen flow, and spatial genetic structure of a natural population of Euterpe precatoria in the Brazilian Amazon.
Santiago Linorio Ferreyra Ramos,Gabriel Dequigiovanni,Alexandre Magno Sebbenn,Maria Teresa Gomes Lopes,Jeferson Luis Vasconcelos de Macêdo,Elizabeth Ann Veasey,Alessandro Alves-Pereira,Perla Pimentel da Silva,José Nivaldo Garcia,Paulo Yoshio Kageyama +9 more
TL;DR: The results indicate substantial allele input in the population via pollen immigration, contributing to the maintenance of the genetic diversity of the population, and within a population, the renewal with new progenies selected from seed plants spaced at least 110 m apart is important to avoid collecting seeds from related plants.
References
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