Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred. For a large majority of replicates for each scenario tested, microsatellite data allow only detecting the recent expansion event in that case, whereas sequence data allow only detecting the ancient expansion. Combined with previous real data analyses, our results bring support to the ideas that (i) a first human expansions started during the Palaeolithic period, (ii) a second expansion event occurred later, concomitantly with the Neolithic transition.
INTRODUCTIONDemographic changes are known to leave footprints on allelic frequencies. Together with the increased availability of large genetic data sets, numerical methods stemming from Kingman's coalescent theory 1 allow inferring the past demography of populations from their present-day patterns of genetic diversity. 2,3 Several types of genetic markers can be used, each category of markers having its own specificities. For instance, as they are uni-parentally transmitted, mitochondrial sequences are informative only about maternal lineages, whereas the Y-chromosome provides information about paternal lineages. In Aimé et al., 4 it has been shown that these two types of markers sometimes provide different inferences on the demographic history of human populations, especially as females generally exhibit higher effective population sizes and higher migration rates than males. 5,6 Conversely, autosomal markers provide synthetic information about both maternal and paternal lineages. When these loci are carefully selected in order to avoid pairwise linkage disequilibria, they also offer the possibility to consider each of them as an independent replicate. Among these autosomal markers, sequences or microsatellites data also exhibit contrasted properties. In particular, microsatellites have higher mutation rates than sequences. 7,8 Moreover, microsatellites are subject to strong homoplasy, which can lead to false signals when using models where this phenomenon is not efficiently controlled for. One simulation-based study 9 showed that when microsatellites are included into an Approximate Bayesian Computation analysis, 10 they provide substantially better estimation for recent admixture events than sequence data. However, they did not investigate the question of inferring other kind of demographic events such as expansions. Moreover, an empirical study on a non-human species (the black sea porpoise) showed that integrating microsatellites in an ABC analy...