Journal ArticleDOI
stratag: An r package for manipulating, summarizing and analysing population genetic data.
TLDR
The r package stratag is introduced as a user‐friendly population genetics toolkit that provides easy access to a suite of standard genetic summaries as well as the ability to rapidly manipulate stratified genetic data for custom analyses.Abstract:
We introduce the r package stratag as a user-friendly population genetics toolkit. stratag provides easy access to a suite of standard genetic summaries as well as the ability to rapidly manipulate stratified genetic data for custom analyses. Tests of population subdivision with most common measures of population subdivision (e.g., FST , GST , ΦST , Χ2 ) can be conducted within a single function. The package also provides wrapper functions that allow users to configure and run popular external programs such as genepop, structure, and fastsimcoal from within r, and smoothly interface with popular r packages adegenet and pegas. stratag is intended to be an open-source dynamic package that will grow with future needs and user input.read more
Citations
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Journal Article
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
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A fast likelihood solution to the genetic clustering problem
TL;DR: Snapclust as discussed by the authors is a fast maximum-likelihood solution to the genetic clustering problem, which allies the advantages of both model-based and geometric approaches, using the Expectation-Maximisation (EM) algorithm.
Journal ArticleDOI
Water, water everywhere: environmental DNA can unlock population structure in elusive marine species
TL;DR: A novel approach for generating population-specific mitochondrial sequence data from environmental DNA (eDNA) using surface seawater samples is developed, exploiting the naturally shed cellular material in seawater and the power of next-generation sequencing.
Journal ArticleDOI
Best Practices for Population Genetic Analyses
TL;DR: This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions and provides resources and examples for analysis in the R programming environment.
Journal ArticleDOI
Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies.
TL;DR: The results of this study show that the original Shannon index should no longer be used as a measure of genetic diversity and should be replaced by Zahl’s unbiased estimator.
References
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Journal Article
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TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Journal ArticleDOI
Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
TL;DR: It is found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters, K, and using an ad hoc statistic ΔK based on the rate of change in the log probability between successive K values, structure accurately detects the uppermost hierarchical level of structure for the scenarios the authors tested.
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Inference of population structure using multilocus genotype data
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