Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex ...

• Main Authors: Ottenburghs, Jente, Honka, Johanna, Heikkinen, Marja E., Madsen, Jesper, Müskens, Gerhard J. D. M., Ellegren, Hans
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: figshare 2024
• Subjects: Genetics; FOS: Biological sciences; Anser brachyrhynchus; Anser fabalis; Pink-footed Goose; taiga; Tundra
• Online Access: https://dx.doi.org/10.6084/m9.figshare.c.6579449.v1; https://springernature.figshare.com/collections/Highly_differentiated_loci_resolve_phylogenetic_relationships_in_the_Bean_Goose_complex/6579449/1

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 ...