• Drosophila;
  • mitochondria;
  • phylogenomics;
  • primates;
  • sex chromosomes

When speciation events occur in rapid succession, incomplete lineage sorting (ILS) can cause disagreement among individual gene trees. The probability that ILS affects a given locus is directly related to its effective population size (Ne), which in turn is proportional to the recombination rate if there is strong selection across the genome. Based on these expectations, we hypothesized that low-recombination regions of the genome, as well as sex chromosomes and nonrecombining chromosomes, should exhibit lower levels of ILS. We tested this hypothesis in phylogenomic datasets from primates, the Drosophila melanogaster clade, and the Drosophila simulans clade. In all three cases, regions of the genome with low or no recombination showed significantly stronger support for the putative species tree, although results from the X chromosome differed among clades. Our results suggest that recurrent selection is acting in these low-recombination regions, such that current levels of diversity also reflect past decreases in the effective population size at these same loci. The results also demonstrate how considering the genomic context of a gene tree can assist in more accurate determination of the true species phylogeny, especially in cases where a whole-genome phylogeny appears to be an unresolvable polytomy.