Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders
- Author
- Lois Rancilhac, Iker Irisarri, Claudio Angelini, Jan W. Arntzen, Wieslaw Babik, Franky Bossuyt, Sven Kuenzel, Tim Lueddecke, Frank Pasmans (UGent) , Eugenia Sanchez, David Weisrock, Michael Veith, Ben Wielstra, Sebastian Steinfartz, Michael Hofreiter, Herve Philippe and Miguel Vences
- Organization
- Abstract
- Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for inter-lineage introgression in the Salamandridae, a Holarctic salamanders group of interest in studies of toxicity and aposematism, courtship behavior, and molecular evolution. Although the relationships between the 21 currently recognized salamandrid genera have been the subject of numerous molecular phylogenetic studies, some branches have remained controversial and sometimes affected by discordances between mitochondrial vs. nuclear trees. To resolve the phylogeny of this family, and understand the source of mitonuclear discordance, we generated new transcriptomic (RNAseq) data for 20 salamandrids and used these along with published data, including 28 mitochondrial genomes, to obtain a comprehensive nuclear and mitochondrial perspective on salamandrid evolution. Our final phylotranscriptomic data set included 5455 gene alignments for 40 species representing 17 of the 21 salamandrid genera. Using concatenation and species-tree phylogenetic methods, we find (1) Salamandrina sister to the clade of the "True Salamanders" (consisting of Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), (2) Ichthyosaura sister to the Near Eastern genera Neurergus and Ommatotriton, (3) Triturus sister to Lissotriton, and (4) Cynops paraphyletic with respect to Paramesotriton and Pachytriton. Combining introgression tests and phylogenetic networks, we find evidence for introgression among taxa within the clades of "Modern Asian Newts" and "Modern European Newts". However, we could not unambiguously identify the number, position, and direction of introgressive events. Combining evidence from nuclear gene analysis with the observed mito-nuclear phylogenetic discordances, we hypothesize a scenario with hybridization and mitochondrial capture among ancestral lineages of (1) Lissotriton into Ichthyosaura and (2) Triturus into Calotriton, plus introgression of nuclear genes from Triturus into Lissotriton. Furthermore, both mitochondrial capture and nuclear introgression may have occurred among lineages assigned to Cynops. More comprehensive genomic data will, in the future, allow testing this against alternative scenarios involving hybridization with other, extinct lineages of newts.
- Keywords
- MAXIMUM-LIKELIHOOD INFERENCE, FAMILY SALAMANDRIDAE, MITOCHONDRIAL-DNA, GENE FLOW, PHYLOGENETIC-RELATIONSHIPS, HYBRID ZONE, EVOLUTION, AMPHIBIA, NUCLEAR, NEWTS, Amphibia, Salamandridae, RNAseq, Phylogenomics, Introgression, Phylogenetic network
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8697920
- MLA
- Rancilhac, Lois, et al. “Phylotranscriptomic Evidence for Pervasive Ancient Hybridization among Old World Salamanders.” MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 155, 2021, doi:10.1016/j.ympev.2020.106967.
- APA
- Rancilhac, L., Irisarri, I., Angelini, C., Arntzen, J. W., Babik, W., Bossuyt, F., … Vences, M. (2021). Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders. MOLECULAR PHYLOGENETICS AND EVOLUTION, 155. https://doi.org/10.1016/j.ympev.2020.106967
- Chicago author-date
- Rancilhac, Lois, Iker Irisarri, Claudio Angelini, Jan W. Arntzen, Wieslaw Babik, Franky Bossuyt, Sven Kuenzel, et al. 2021. “Phylotranscriptomic Evidence for Pervasive Ancient Hybridization among Old World Salamanders.” MOLECULAR PHYLOGENETICS AND EVOLUTION 155. https://doi.org/10.1016/j.ympev.2020.106967.
- Chicago author-date (all authors)
- Rancilhac, Lois, Iker Irisarri, Claudio Angelini, Jan W. Arntzen, Wieslaw Babik, Franky Bossuyt, Sven Kuenzel, Tim Lueddecke, Frank Pasmans, Eugenia Sanchez, David Weisrock, Michael Veith, Ben Wielstra, Sebastian Steinfartz, Michael Hofreiter, Herve Philippe, and Miguel Vences. 2021. “Phylotranscriptomic Evidence for Pervasive Ancient Hybridization among Old World Salamanders.” MOLECULAR PHYLOGENETICS AND EVOLUTION 155. doi:10.1016/j.ympev.2020.106967.
- Vancouver
- 1.Rancilhac L, Irisarri I, Angelini C, Arntzen JW, Babik W, Bossuyt F, et al. Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders. MOLECULAR PHYLOGENETICS AND EVOLUTION. 2021;155.
- IEEE
- [1]L. Rancilhac et al., “Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders,” MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 155, 2021.
@article{8697920, abstract = {{Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for inter-lineage introgression in the Salamandridae, a Holarctic salamanders group of interest in studies of toxicity and aposematism, courtship behavior, and molecular evolution. Although the relationships between the 21 currently recognized salamandrid genera have been the subject of numerous molecular phylogenetic studies, some branches have remained controversial and sometimes affected by discordances between mitochondrial vs. nuclear trees. To resolve the phylogeny of this family, and understand the source of mitonuclear discordance, we generated new transcriptomic (RNAseq) data for 20 salamandrids and used these along with published data, including 28 mitochondrial genomes, to obtain a comprehensive nuclear and mitochondrial perspective on salamandrid evolution. Our final phylotranscriptomic data set included 5455 gene alignments for 40 species representing 17 of the 21 salamandrid genera. Using concatenation and species-tree phylogenetic methods, we find (1) Salamandrina sister to the clade of the "True Salamanders" (consisting of Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), (2) Ichthyosaura sister to the Near Eastern genera Neurergus and Ommatotriton, (3) Triturus sister to Lissotriton, and (4) Cynops paraphyletic with respect to Paramesotriton and Pachytriton. Combining introgression tests and phylogenetic networks, we find evidence for introgression among taxa within the clades of "Modern Asian Newts" and "Modern European Newts". However, we could not unambiguously identify the number, position, and direction of introgressive events. Combining evidence from nuclear gene analysis with the observed mito-nuclear phylogenetic discordances, we hypothesize a scenario with hybridization and mitochondrial capture among ancestral lineages of (1) Lissotriton into Ichthyosaura and (2) Triturus into Calotriton, plus introgression of nuclear genes from Triturus into Lissotriton. Furthermore, both mitochondrial capture and nuclear introgression may have occurred among lineages assigned to Cynops. More comprehensive genomic data will, in the future, allow testing this against alternative scenarios involving hybridization with other, extinct lineages of newts.}}, articleno = {{106967}}, author = {{Rancilhac, Lois and Irisarri, Iker and Angelini, Claudio and Arntzen, Jan W. and Babik, Wieslaw and Bossuyt, Franky and Kuenzel, Sven and Lueddecke, Tim and Pasmans, Frank and Sanchez, Eugenia and Weisrock, David and Veith, Michael and Wielstra, Ben and Steinfartz, Sebastian and Hofreiter, Michael and Philippe, Herve and Vences, Miguel}}, issn = {{1055-7903}}, journal = {{MOLECULAR PHYLOGENETICS AND EVOLUTION}}, keywords = {{MAXIMUM-LIKELIHOOD INFERENCE,FAMILY SALAMANDRIDAE,MITOCHONDRIAL-DNA,GENE FLOW,PHYLOGENETIC-RELATIONSHIPS,HYBRID ZONE,EVOLUTION,AMPHIBIA,NUCLEAR,NEWTS,Amphibia,Salamandridae,RNAseq,Phylogenomics,Introgression,Phylogenetic network}}, language = {{eng}}, pages = {{14}}, title = {{Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders}}, url = {{http://doi.org/10.1016/j.ympev.2020.106967}}, volume = {{155}}, year = {{2021}}, }
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