Y-chromosome mismatch distributions in Europe

Ancient demographic events can be inferred from the distribution of pairwis e sequence differences (or mismatches) among individuals. We analyzed a dat abase of 3,677 Y chromosomes typed for 11 biallelic markers in 48 human pop ulations from Europe and the Mediterranean area. Contrary to what is observ ed in the analysis of mitochondrial polymorphisms, Tajima's test was insign ificant for most Y-chromosome samples, and in 47 populations the mismatch d istributions had multiple peaks. Taken at face value, these results would s uggest either (1) that the size of the male population stayed essentially c onstant over time, while the female population size increased, or (2) that different selective regimes have shaped mitochondrial and Y-chromosome dive rsity, leading to an excess of rare alleles only in the mitochondrial genom e. An alternative explanation would be that the Il variable sites of the Y chromosome do not provide sufficient statistical power, so a comparison wit h mitochondrial data (where more than 200 variable sites are studied in Eur ope) is impossible at present. To discriminate between these possibilities, we repeatedly analyzed a European mitochondrial database, each time consid ering only 11 variable sites, and we estimated mismatch distributions in st able and growing populations, generated by simulating coalescent processes. Along with theoretical considerations, these tests suggest that the differ ence between the mismatch distributions inferred from mitochondrial and Y-c hromosome data are not a statistical artifact. Therefore, the observed mism atch distributions appear to reflect different underlying demographic histo ries and/or selective pressures for maternally and paternally transmitted l oci.