Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex
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 t...
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Uppsala universitet, Evolutionsbiologi
2023
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ftuppsalauniv:oai:DiVA.org:uu-496583 2024-01-14T09:59:24+01:00 Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex Ottenburghs, Jente Honka, Johanna Heikkinen, Marja E. Madsen, Jesper Müskens, Gerhard J. D. M. Ellegren, Hans 2023 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-496583 https://doi.org/10.1186/s12862-023-02103-3 eng eng Uppsala universitet, Evolutionsbiologi Univ Oulu, Ecol & Genet Res Unit, POB 3000, Oulu 90014, Finland. Aarhus Univ, Dept Ecosci, CF Mollers Alle 8, DK-8000 Aarhus C, Denmark. Wageningen Univ & Res, Wageningen Environm Res, Team Anim Ecol, Droevendaalsesteeg 3-3A, NL-6708 PB Wageningen, Netherlands. BMC Ecology and Evolution, 2023, 23, orcid:0000-0002-0335-9655 orcid:0000-0002-7051-5654 orcid:0000-0002-5035-1736 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-496583 doi:10.1186/s12862-023-02103-3 PMID 36658479 ISI:000916433700001 info:eu-repo/semantics/openAccess Anseriformes Introgression Differentiation islands Phylogenomics Species tree Evolutionary Biology Evolutionsbiologi Article in journal info:eu-repo/semantics/article text 2023 ftuppsalauniv https://doi.org/10.1186/s12862-023-02103-3 2023-12-20T23:31:55Z 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 ... Article in Journal/Newspaper Anser brachyrhynchus Anser fabalis Pink-footed Goose taiga Tundra Uppsala University: Publications (DiVA) BMC Ecology and Evolution 23 1 |
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Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Anseriformes Introgression Differentiation islands Phylogenomics Species tree Evolutionary Biology Evolutionsbiologi |
spellingShingle |
Anseriformes Introgression Differentiation islands Phylogenomics Species tree Evolutionary Biology Evolutionsbiologi Ottenburghs, Jente Honka, Johanna Heikkinen, Marja E. Madsen, Jesper Müskens, Gerhard J. D. M. Ellegren, Hans Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex |
topic_facet |
Anseriformes Introgression Differentiation islands Phylogenomics Species tree Evolutionary Biology Evolutionsbiologi |
description |
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 ... |
format |
Article in Journal/Newspaper |
author |
Ottenburghs, Jente Honka, Johanna Heikkinen, Marja E. Madsen, Jesper Müskens, Gerhard J. D. M. Ellegren, Hans |
author_facet |
Ottenburghs, Jente Honka, Johanna Heikkinen, Marja E. Madsen, Jesper Müskens, Gerhard J. D. M. Ellegren, Hans |
author_sort |
Ottenburghs, Jente |
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 |
Uppsala universitet, Evolutionsbiologi |
publishDate |
2023 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-496583 https://doi.org/10.1186/s12862-023-02103-3 |
genre |
Anser brachyrhynchus Anser fabalis Pink-footed Goose taiga Tundra |
genre_facet |
Anser brachyrhynchus Anser fabalis Pink-footed Goose taiga Tundra |
op_relation |
BMC Ecology and Evolution, 2023, 23, orcid:0000-0002-0335-9655 orcid:0000-0002-7051-5654 orcid:0000-0002-5035-1736 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-496583 doi:10.1186/s12862-023-02103-3 PMID 36658479 ISI:000916433700001 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1186/s12862-023-02103-3 |
container_title |
BMC Ecology and Evolution |
container_volume |
23 |
container_issue |
1 |
_version_ |
1788058997422555136 |