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  Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders

Rancilhac, L., Irisarri, I., Angelini, C., Arntzen, J., Babik, W., Bossuyt, F., et al. (2020). Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders. Molecular Phylogenetics and Evolution, n/a(n/a): 106967. doi:10.1016/j.ympev.2020.106967.

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 Creators:
Rancilhac, L., Author
Irisarri, I., Author
Angelini, C., Author
Arntzen, J.W., Author
Babik, W., Author
Bossuyt, F., Author
Künzel, S.1, Author              
Lüddecke, T., Author
Pasmans, F., Author
Sanchez, E., Author
Weisrock, D., Author
Veith, M., Author
Wielstra, B., Author
Steinfartz, S., Author
Hofreiter, M., Author
Philippe, H., Author
Vences, M., Author
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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Free keywords: Amphibia; Introgression; Phylogenetic network; Phylogenomics; RNAseq; Salamandridae
 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 mito-nuclear 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. © 2020 Elsevier Inc.

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Language(s): eng - English
 Dates: 2020-07-092019-12-172020-09-282020-10-062020
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1016/j.ympev.2020.106967
 Degree: -

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Title: Molecular Phylogenetics and Evolution
Source Genre: Journal
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Publ. Info: Orlando, Fla. : Academic Press
Pages: - Volume / Issue: n/a (n/a) Sequence Number: 106967 Start / End Page: - Identifier: ISSN: 1055-7903
CoNE: https://pure.mpg.de/cone/journals/resource/954922650168