Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils
Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological...
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PeerJ Inc.
2018-07-01
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| Online Access: | https://peerj.com/articles/5168.pdf |
| _version_ | 1797418539691278336 |
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| author | Justin C. Bagley Richard L. Mayden Phillip M. Harris |
| author_facet | Justin C. Bagley Richard L. Mayden Phillip M. Harris |
| author_sort | Justin C. Bagley |
| collection | DOAJ |
| description | Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning. |
| first_indexed | 2024-03-09T06:35:19Z |
| format | Article |
| id | doaj.art-955527f46ad24d3aa2280b224eb4d633 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:35:19Z |
| publishDate | 2018-07-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-955527f46ad24d3aa2280b224eb4d6332023-12-03T11:00:03ZengPeerJ Inc.PeerJ2167-83592018-07-016e516810.7717/peerj.5168Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossilsJustin C. Bagley0Richard L. Mayden1Phillip M. Harris2Department of Biology, Virginia Commonwealth University, Richmond, VA, USADepartment of Biology, Saint Louis University, St. Louis, MO, USADepartment of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USACatostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.https://peerj.com/articles/5168.pdfMolecular phylogeneticsCatostomidaeFossilized birth-death processDivergence time estimationRelaxed molecular clockPhylogenetic informativeness profiles |
| spellingShingle | Justin C. Bagley Richard L. Mayden Phillip M. Harris Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils PeerJ Molecular phylogenetics Catostomidae Fossilized birth-death process Divergence time estimation Relaxed molecular clock Phylogenetic informativeness profiles |
| title | Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
| title_full | Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
| title_fullStr | Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
| title_full_unstemmed | Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
| title_short | Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils |
| title_sort | phylogeny and divergence times of suckers cypriniformes catostomidae inferred from bayesian total evidence analyses of molecules morphology and fossils |
| topic | Molecular phylogenetics Catostomidae Fossilized birth-death process Divergence time estimation Relaxed molecular clock Phylogenetic informativeness profiles |
| url | https://peerj.com/articles/5168.pdf |
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