Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex
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 tha...
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ftdoajarticles:oai:doaj.org/article:417cf3e3880f485480fe283d51f3725d 2023-05-15T13:29:59+02:00 Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex Jente Ottenburghs Johanna Honka Marja E. Heikkinen Jesper Madsen Gerhard J. D. M. Müskens Hans Ellegren 2023-01-01T00:00:00Z https://doi.org/10.1186/s12862-023-02103-3 https://doaj.org/article/417cf3e3880f485480fe283d51f3725d EN eng BMC https://doi.org/10.1186/s12862-023-02103-3 https://doaj.org/toc/2730-7182 doi:10.1186/s12862-023-02103-3 2730-7182 https://doaj.org/article/417cf3e3880f485480fe283d51f3725d BMC Ecology and Evolution, Vol 23, Iss 1, Pp 1-12 (2023) Anseriformes Introgression Differentiation islands Phylogenomics Species tree Ecology QH540-549.5 Evolution QH359-425 article 2023 ftdoajarticles https://doi.org/10.1186/s12862-023-02103-3 2023-01-29T01:31:34Z 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 ... Article in Journal/Newspaper Anser brachyrhynchus Anser fabalis Pink-footed Goose taiga Tundra Directory of Open Access Journals: DOAJ Articles BMC Ecology and Evolution 23 1 |
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Open Polar |
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op_collection_id |
ftdoajarticles |
language |
English |
topic |
Anseriformes Introgression Differentiation islands Phylogenomics Species tree Ecology QH540-549.5 Evolution QH359-425 |
spellingShingle |
Anseriformes Introgression Differentiation islands Phylogenomics Species tree Ecology QH540-549.5 Evolution QH359-425 Jente Ottenburghs Johanna Honka Marja E. Heikkinen Jesper Madsen Gerhard J. D. M. Müskens Hans Ellegren Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
topic_facet |
Anseriformes Introgression Differentiation islands Phylogenomics Species tree Ecology QH540-549.5 Evolution QH359-425 |
description |
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 ... |
format |
Article in Journal/Newspaper |
author |
Jente Ottenburghs Johanna Honka Marja E. Heikkinen Jesper Madsen Gerhard J. D. M. Müskens Hans Ellegren |
author_facet |
Jente Ottenburghs Johanna Honka Marja E. Heikkinen Jesper Madsen Gerhard J. D. M. Müskens Hans Ellegren |
author_sort |
Jente Ottenburghs |
title |
Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
title_short |
Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
title_full |
Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
title_fullStr |
Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
title_full_unstemmed |
Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
title_sort |
highly differentiated loci resolve phylogenetic relationships in the bean goose complex |
publisher |
BMC |
publishDate |
2023 |
url |
https://doi.org/10.1186/s12862-023-02103-3 https://doaj.org/article/417cf3e3880f485480fe283d51f3725d |
genre |
Anser brachyrhynchus Anser fabalis Pink-footed Goose taiga Tundra |
genre_facet |
Anser brachyrhynchus Anser fabalis Pink-footed Goose taiga Tundra |
op_source |
BMC Ecology and Evolution, Vol 23, Iss 1, Pp 1-12 (2023) |
op_relation |
https://doi.org/10.1186/s12862-023-02103-3 https://doaj.org/toc/2730-7182 doi:10.1186/s12862-023-02103-3 2730-7182 https://doaj.org/article/417cf3e3880f485480fe283d51f3725d |
op_doi |
https://doi.org/10.1186/s12862-023-02103-3 |
container_title |
BMC Ecology and Evolution |
container_volume |
23 |
container_issue |
1 |
_version_ |
1766004700121923584 |