Different genomic regions may reflect conflicting phylogenetic topologies on account of incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Phylogenetic analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal that the northern and southern populations of E. godlewskii are each sister to E. cioides and E. cia, respectively. In contrast, phylogenetic analysis based on genome-wide data support the monophyly of E. godlewskii with the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data and mtDNA/W trees. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.

Dataset and supporting information from the manuscript of Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae).