University of Oulu

Ottenburghs, J., Honka, J., Heikkinen, M.E. et al. Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecol Evo 23, 2 (2023).

Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex

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Author: Ottenburghs, Jente1; Honka, Johanna2; Heikkinen, Marja E.2;
Organizations: 1Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
2Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014, Oulu, Finland
3Department of Ecoscience, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
4Team Animal Ecology, Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3-3A, 6708 PB, Wageningen, The Netherlands
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.3 MB)
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Language: English
Published: Springer Nature, 2023
Publish Date: 2023-08-10


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 pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree.

Conclusions: The evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.

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Series: BMC ecology and evolution
ISSN: 2730-7182
ISSN-E: 2730-7182
ISSN-L: 2730-7182
Volume: 23
Issue: 1
Article number: 2
DOI: 10.1186/s12862-023-02103-3
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Funding: Open access funding provided by Uppsala University. This research was made possible by grants from the Swedish Research Council (contract 2013-8271) and the Knut and Alice Wallenberg foundation (contract 2014.0044).
Copyright information: Ottenburghs et al. © The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated in a credit line to the data.