Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method

The species divergence times and demographic histories of Drosophila melano gaster and its three sibling species, D. mauritiana, D. simulans, and D. ya kuba, were investigated using a maximum likelihood (ML) method. Thirty-nine orthologous loci for these four species were retrieved from DDBJ/EMBL/GenB ank database. Both autosomal and X-linked loci were used in this study. A s ignificant degree of rate heterogeneity across loci was observed for each p air of species. Most loci have the GC content greater than 50% at the third codon position. The codon usage bias in Drosophila loci is considered to r esult in the high GC content and the heterogenous rates across loci. The ch i-square, G, and Fisher's exact tests indicated that data sets with 11, 23, and 9 pairs of DNA sequences for the comparison of D. melanogaster with D. mauritiana, D. simulans, and D. yakuba, respectively, retain homogeneous r ates across loci. We applied the ML method to these data sets to estimate t he DNA sequence divergences before and after speciation of each species pai r along with their standard deviations. Using 1.6 x 10(-8) as the rate of n ucleotide substitutions per silent site per year, our results indicate that the D. melanogaster lineage split from D. yakuba approximately 5.1 +/- 0.8 million years ago (mya), D. mauritiana 2.7 +/- 0.4 mya, and D. simulans 2. 3 +/- 0.3 mya. It implies that D. melanogaster became distinct from D. maur itiana and D. simulans at approximately the same time and from D. yakuba no earlier than 10 mya. The effective ancestral population size of D. melanog aster appears to be stable over evolutionary time. Assuming 10 generations per year for Drosophila, the effective population size in the ancestral lin eage immediately prior to the time of species divergence is approximately 3 x 10(6), which is close to that estimated for the extant D. melanogaster p opulation. The D. melanogaster did not encounter any obvious bottleneck dur ing the past 10 million years.