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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.
Most genetic studies on non-model organisms require a description of the pattern of diversity within and between populations, based on a variety of markers often including mitochondrial DNA (mtDNA) sequences and microsatellites. The genetic data are processed to extract information on the mating system, the extent of population subdivision, the past demography of the population, or on departure from selective neutrality at some loci. A series of computer packages have been developed in the last 10 years to assist researchers in performing basic population genetics analyses like Arlequin2 (Schneider et al. 2000), DNASP (Rozas et al. 2003), FSTAT (Goudet 1995), GENEPOP (Raymond and Rousset 1995b), or GENETIX (Belkhir et al. 2004). These programs have been widely used in the molecular ecology and conservation genetics community (Labate 2000; Luikart and England 1999; Schnabel et al. 1998). Among these, Arlequin is a very versatile (though not universal) program, and complements the other programs listed above. It can handle several data types like RFLPs, DNA sequences, microsatellite data, allele frequencies, or standard multi-locus genotypes, while allowing the user to carry out the same types of analyses irrespective of the data types.
We present here the version 3 of Arlequin with additional methods extending its capacities for the handling of unphased multi-locus genotypes and for the estimation of parameters of a spatial expansion. Note that these new developments are mainly implementations of new methodologies developed in our lab. We believe these methods will be useful to the research community, but we do not claim that alternative methods implemented by other groups in other programs are inadequate. A new graphical interface has been developed to provide a better integration of the different analyses into a common framework, and an easier exploration of the data by performing a wide variety of analyses with different settings. The tight coupling of Arlequin with the simulation programs SIMCOAL2 (Laval and Excoffier 2004) and SPLATCHE (Currat et al. 2004) should also make it useful to describe patterns of genetic diversity under complex evolutionary scenarios.
Arlequin provides methods to analyse patterns of genetic diversity within and between population samples.
A Windows executable version Arlequin ver 3 can be freely downloaded on http://cmpg.unibe.ch/software/arlequin3, together with an up-to-date user manual in Adobe Acrobat PDF format incorporating more technical details on the methods used in Arlequin 3, as well as several example files.
This work was partially made possible thanks to a Swiss NSF grant No 31-56755.99 to LE.