Journal ArticleDOI
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
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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.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.read more
Citations
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Eurasian house mouse ( Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot
Emilie A. Hardouin,Emilie A. Hardouin,Annie Orth,Meike Teschke,Jamshid Darvish,Diethard Tautz,François Bonhomme +6 more
TL;DR: It is proposed that the Iranian plateau is home to two more taxonomic units displaying complex primary and secondary relationships with their long recognized neighbours, designating it as the focal place to study the mechanisms of speciation and diversification of this species.
Journal ArticleDOI
Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries
Giuseppe Iacovacci,Eugenia D'Atanasio,Ornella Marini,Alfredo Coppa,Daniele Sellitto,Beniamino Trombetta,Andrea Berti,Fulvio Cruciani +7 more
TL;DR: The strong population subdivision observed is probably the consequence of the patrilineal social organization of most eastern African ethnic groups, and suggests caution in the use of country-based haplotype frequency distributions for forensic inferences in this region.
Journal ArticleDOI
The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age
Anna Szécsényi-Nagy,Christina Roth,Guido Brandt,Cristina Rihuete-Herrada,Cristina Tejedor-Rodríguez,Petra Held,Íñigo García-Martínez-de-Lagrán,Héctor Arcusa Magallón,Stephanie Zesch,Corina Knipper,Eszter Bánffy,Susanne Friederich,Harald Meller,Primitiva Bueno Ramírez,Rosa María Barroso Bermejo,Rodrigo de Balbín Behrmann,Ana Mercedes Herrero-Corral,Raúl Flores Fernández,Carmen Alonso Fernández,Javier Jiménez Echevarría,Laura Rindlisbacher,Camila Oliart,María-Inés Fregeiro,Ignacio Soriano,Oriol Vicente,Rafael Micó,Vicente Lull,J. S. Díaz,Juan Antonio López Padilla,Consuelo Roca de Togores Muñoz,Mauro S. Hernández Pérez,Francisco Javier Jover Maestre,Joaquín Lomba Maurandi,Azucena Avilés Fernández,Katina T. Lillios,Ana Maria Silva,Ana Maria Silva,Miguel Magalhães Ramalho,Luiz Oosterbeek,Claudia Cunha,Anna J. Waterman,Jordi Roig Buxó,Andrés Martínez,Juana Ponce martínez,Mark A. Hunt Ortiz,Juan Carlos Mejías-García,Juan Carlos Pecero Espín,Rosario Cruz-Auñón Briones,Tiago Tomé,Eduardo Carmona Ballestero,João Luís Cardoso,Ana Cristina Araújo,Corina Liesau von Lettow-Vorbeck,Concepción Blasco Bosqued,Patricia Ríos Mendoza,Ana Pujante,José I. Royo-Guillén,Marco Aurelio Esquembre Beviá,Victor S. Gonçalves,Rui Parreira,Elena Morán Hernández,Elena Méndez Izquierdo,Jorge Vega de Miguel,Roberto Menduiña García,Victoria Martínez Calvo,Oscar López Jiménez,Johannes Krause,Sandra Pichler,Rafael Garrido-Pena,Michael Kunst,Roberto Risch,Manuel Rojo-Guerra,Wolfgang Haak,Wolfgang Haak,Kurt W. Alt,Kurt W. Alt +75 more
TL;DR: This study focuses on the maternal genetic makeup of the Neolithic, Chalcolithic and Early Bronze Age in Iberia, and reports ancient mitochondrial DNA results of 213 individuals from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date.
Journal ArticleDOI
Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana.
Yuan Chen,Anastasia P. Litvintseva,Aubrey E. Frazzitta,Miriam Haverkamp,Liuyang Wang,Charles Fang,Charles Muthoga,Thomas G. Mitchell,John R. Perfect +8 more
TL;DR: Significant genetic diversity among isolates and strong evidence of geographic structure at the local level are detected, providing a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.
Journal ArticleDOI
A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds
Arianna Manunza,Antonia Noce,Juan Manuel Serradilla,Félix Goyache,Amparo Martínez Martínez,Juan Capote,Juan Vicente Delgado,Jordi Jordana,Eva Muñoz,Antonio Molina,Vincenzo Landi,A. Pons,Valentin A. Balteanu,Amadou Traoré,Montse Vidilla,Manuel Sánchez-Rodríguez,Armand Sánchez,Tainã Figueiredo Cardoso,Marcel Amills +18 more
TL;DR: Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work, generating distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations.
References
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Journal ArticleDOI
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Journal ArticleDOI
Arlequin (version 3.0): An integrated software package for population genetics data analysis
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.
Journal ArticleDOI
Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Journal ArticleDOI
Evaluating Loci for Use in the Genetic Analysis of Population Structure
TL;DR: It is suggested that genetic variation at a discrepant locus, Identified under these conditions, is likely to have been influenced by natural selection, either acting on the locus itself or at a closely linked locus.
Journal ArticleDOI
Detection of reduction in population size using data from microsatellite loci.
TL;DR: It is demonstrated that the mean ratio of the number of alleles to the range in allele size, which is calculated from a population sample of microsatellite loci, can be used to detect reductions in population size and that the value of M consistently predicts the reported demographic history for these populations.