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Journal ArticleDOI

Arlequin (version 3.0): An integrated software package for population genetics data analysis

01 Jan 2005-Evolutionary Bioinformatics (Libertas Academica)-Vol. 1, Iss: 1, pp 47-50
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Abstract: Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces 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. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

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Citations
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Journal ArticleDOI
TL;DR: 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.
Abstract: We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version 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. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.

13,581 citations

Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
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.

11,521 citations

Journal ArticleDOI

3,734 citations

Journal ArticleDOI
TL;DR: Popart is presented, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production.
Abstract: Summary Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. The software is open source and freely available for all major operating systems.

3,634 citations

Journal ArticleDOI
Riccardo Velasco, Andrey Zharkikh1, Jason P. Affourtit2, Amit Dhingra3, Alessandro Cestaro, Ananth Kalyanaraman3, Paolo Fontana, Satish Bhatnagar1, Michela Troggio, Dmitry Pruss1, Silvio Salvi4, Massimo Pindo, Paolo Baldi, Sara Castelletti, Marina Cavaiuolo, G. Coppola, Fabrizio Costa, V. Cova, Antonio Dal Ri, Vadim V. Goremykin, M. Komjanc, Sara Longhi, P. Magnago, Giulia Malacarne, Mickael Malnoy, Diego Micheletti, Marco Moretto, Michele Perazzolli, Azeddine Si-Ammour, Silvia Vezzulli, E. Zini, Glenn Eldredge1, Lisa M. Fitzgerald1, N. Gutin1, Jerry S. Lanchbury1, Teresita Macalma1, J.T. Mitchell1, Julia Reid1, Bryan Wardell1, Chinnappa D. Kodira2, Zhoutao Chen2, Brian Desany2, Faheem Niazi2, Melinda Palmer2, Tyson Koepke3, Derick Jiwan3, Scott Schaeffer3, Vandhana Krishnan3, Changjun Wu3, Vu T. Chu5, Stephen T. King5, Jessica Vick5, Quanzhou Tao, Amy Mraz, Aimee Stormo, Keith E. Stormo, Robert Bogden, Davide Ederle6, Alessandra Stella6, Alberto Vecchietti6, Martin M. Kater7, Simona Masiero7, Pauline Lasserre, Yves Lespinasse, Andrew C. Allan8, Vincent G. M. Bus8, David Chagné8, Ross N. Crowhurst8, Andrew P. Gleave8, Enrico Lavezzo9, Jeffrey A. Fawcett10, Jeffrey A. Fawcett11, Sebastian Proost10, Sebastian Proost11, Pierre Rouzé11, Pierre Rouzé10, Lieven Sterck10, Lieven Sterck11, Stefano Toppo9, Barbara Lazzari6, Roger P. Hellens8, Charles-Eric Durel, Alexander Gutin1, Roger E. Bumgarner5, Susan E. Gardiner8, Mark H. Skolnick1, Michael Egholm2, Yves Van de Peer10, Yves Van de Peer11, Francesco Salamini6, Roberto Viola 
TL;DR: It is shown that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae, which partly support the monophyly of the ancestral paleohexaploidy of eudicots.
Abstract: We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.

1,718 citations

References
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Book
01 Jan 1993
TL;DR: This article presents bootstrap methods for estimation, using simple arguments, with Minitab macros for implementing these methods, as well as some examples of how these methods could be used for estimation purposes.
Abstract: This article presents bootstrap methods for estimation, using simple arguments. Minitab macros for implementing these methods are given.

37,183 citations

Journal ArticleDOI
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Abstract: Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or “transition” type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or “transversion” type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

26,016 citations

Journal ArticleDOI
TL;DR: The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973).
Abstract: This journal frequently contains papers that report values of F-statistics estimated from genetic data collected from several populations. These parameters, FST, FIT, and FIS, were introduced by Wright (1951), and offer a convenient means of summarizing population structure. While there is some disagreement about the interpretation of the quantities, there is considerably more disagreement on the method of evaluating them. Different authors make different assumptions about sample sizes or numbers of populations and handle the difficulties of multiple alleles and unequal sample sizes in different ways. Wright himself, for example, did not consider the effects of finite sample size. The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973). We start with the parameters and construct appropriate estimators for them, rather than beginning the discussion with various data functions. The extension of Cockerham's work to multiple alleles and loci will be made explicit, and the use of jackknife procedures for estimating variances will be advocated. All of this may be regarded as an extension of a recent treatment of estimating the coancestry coefficient to serve as a mea-

17,890 citations

Book
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.

15,840 citations