Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Reconstructing species trees from genomic data is challenging due to incongruent gene trees.
• Highly divergent genomic regions ('differentiation islands') are proposed to reflect species trees, but can be misleading.
• The Bean Goose complex (Anser fabalis, Anser serrirostris, Anser brachyrhynchus) serves as a model system.

Purpose of the Study:

• To assess the utility of highly differentiated genomic loci for resolving phylogenetic relationships.
• To investigate the impact of introgression on phylogenetic signal in the Bean Goose complex.

Main Methods:

• Phylogenetic analyses using random genomic loci versus differentiation islands.
• Analysis of locus trees within differentiated regions.
• D-statistics to detect introgression between Anser fabalis and Anser serrirostris.

Main Results:

• Random genomic loci failed to resolve the species complex, yielding a paraphyletic arrangement.
• Phylogenetic analyses of differentiation islands consistently recovered a topology of three monophyletic clades.
• Extensive introgression between Anser fabalis and Anser serrirostris was detected, obscuring phylogenetic signal in undifferentiated regions.

Conclusions:

• Highly differentiated loci accurately reflect the species tree of the Bean Goose complex.
• Introgressive hybridization significantly impacts phylogenetic reconstruction, necessitating alternative representations.
• Phylogenetic networks are advocated to represent the complex evolutionary history of these taxa.