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





The species divergence times and demographic histories of <i>Drosophila melanogaster</i> and its three sibling species, <i>D. mauritiana</i>, <i>D. simulans</i>, and <i>D. yakuba</i>, were investigated using a maximum likelihood (ML) method. Thirty-nine orthologous loci for these four species were retrieved from DDBJ/EMBL/GenBank database. Both autosomal and X-linked loci were used in this study. A significant degree of rate heterogeneity across loci was observed for each pair of species. Most loci have the GC content greater than 50% at the third codon position. The codon usage bias in <i>Drosophila</i> loci is considered to result in the high GC content and the heterogenous rates across loci. The chi-square, G, and Fisher's exact tests indicated that data sets with 11, 23, and 9 pairs of DNA sequences for the comparison of <i>D. melanogaster</i> with <i>D. mauritiana</i>, <i>D. simulans</i>, and <i>D. yakuba</i>, respectively, retain homogeneous rates across loci. We applied the ML method to these data sets to estimate the DNA sequence divergences before and after speciation of each species pair along with their standard deviations. Using 1.6 × 10<sup>-8</sup> as the rate of nucleotide substitutions per silent site per year, our results indicate that the <i>D. melanogaster</i> lineage split from <i>D. yakuba</i> approximately 5.1 ± 0.8 million years ago (mya), <i>D. mauritiana</i> 2.7 ± 0.4 mya, and <i>D. simulans</i> 2.3 ± 0.3 mya. It implies that <i>D. melanogaster</i> became distinct from <i>D. mauritiana</i> and <i>D. simulans</i> at approximately the same time and from <i>D. yakuba</i> no earlier than 10 mya. The effective ancestral population size of <i>D. melanogaster</i> appears to be stable over evolutionary time. Assuming 10 generations per year for <i>Drosophila</i>, the effective population size in the ancestral lineage immediately prior to the time of species divergence is approximately 3 × 10<sup>6</sup>, which is close to that estimated for the extant <i>D. melanogaster</i> population. The <i>D. melanogaster</i> did not encounter any obvious bottleneck during the past 10 million years.<br>


  • Genes & genetic systems

    Genes & genetic systems 74(4), 117-127, 1999-08

    The Genetics Society of Japan

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