title: Combining contemporary and ancient DNA in population genetic and phylogeographical studies.
abstract: The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed.
authors.affiliation: INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, F-34988 Montferrier-sur-Lez Cedex, France Laboratoire Ecologie et Evolution, CNRS UMR 7625, UPMC Paris Universitas, Ecole Normale Supérieure, Paris, France Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
authors.forename: Miguel
authors.initials: M
authors.lastname: Navascués
authors.forename: Frantz
authors.initials: F
authors.lastname: Depaulis
authors.forename: Brent C
authors.initials: BC
authors.lastname: Emerson