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Arlequin (version 3.0): An integrated software package for population genetics data analysis
TLDR
A completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism are introduced. Expand
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
TLDR
Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis, and Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. Expand
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
TLDR
The main innovations of the new version of the Arlequin program include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Expand
Arlequin (version 3.0): An integrated software package for population genetics data analysis
TLDR
A completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism are introduced. Expand
A simulated annealing approach to define the genetic structure of populations
TLDR
The samova algorithm was applied to a set of European roe deer populations examined for their mitochondrial DNA (mtDNA) HVRI diversity and the inferred genetic structure seemed to confirm the hypothesis that some Italian populations were recently reintroduced from a Balkanic stock. Expand
Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA.
TLDR
This article shows how to infer past demographic parameters by explicitly taking into account a finite-sites model with heterogeneity of mutation rates, and proposes an alternative way to derive confidence intervals around the estimated parameters, based on a bootstrap approach. Expand
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs
TLDR
PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats, is introduced, allowing its integration in complex data analysis pipelines. Expand
Detecting loci under selection in a hierarchically structured population
TLDR
It is shown that tests not accounting for a hierarchical structure, when it exists, do generate a large excess of false positive loci, whereas the hierarchical island model is robust to uncertainties about the exact number of groups and demes per group in the system. Expand
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.
TLDR
An expectation-maximization (EM) algorithm leading to maximum-likelihood estimates of molecular haplotype frequencies under the assumption of Hardy-Weinberg proportions is implemented and appears to be useful for the analysis of nuclear DNA sequences or highly variable loci. Expand
Robust Demographic Inference from Genomic and SNP Data
TLDR
A flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets and shows that it allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. Expand
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