Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex

• Published in: BMC Ecology and Evolution
• Main Authors: Jente Ottenburghs, Johanna Honka, Marja E. Heikkinen, Jesper Madsen, Gerhard J. D. M. Müskens, Hans Ellegren
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2023
• Subjects: Anseriformes; Introgression; Differentiation islands; Phylogenomics; Species tree; Ecology; QH540-549.5; Evolution; QH359-425; Anser brachyrhynchus; Anser fabalis; Pink-footed Goose; taiga; Tundra
• Online Access: https://doi.org/10.1186/s12862-023-02103-3; https://doaj.org/article/417cf3e3880f485480fe283d51f3725d

Abstract Background Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a ‘true’ species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus). Results First, we show that a random selection of genomic loci—which mainly samples the undifferentiated regions of the genome—results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the ‘true’ species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching ...