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  Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches

Rodríguez, A., Burgon, J. D., Lyra, M., Irisarri, I., Baurain, D., Blaustein, L., et al. (2017). Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Molecular Phylogenetics and Evolution, 115, 16-26. doi:10.1016/j.ympev.2017.07.009.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002E-2C92-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002E-2C93-8
Genre: Journal Article

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 Creators:
Rodríguez, Ariel, Author
Burgon, James D., Author
Lyra, Mariana, Author
Irisarri, Iker, Author
Baurain, Denis, Author
Blaustein, Leon, Author
Göçmen, Bayram, Author
Künzel, Sven1, Author              
Mable, Barbara K., Author
Nolte, Arne W.2, Author              
Veith, Michael, Author
Steinfartz, Sebastian, Author
Elmer, Kathryn R., Author
Philippe, Hervé, Author
Vences, Miguel, Author
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              
2Research Group Evolutionary Genetics of Fishes, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445645              

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Free keywords: Amphibia; Caudata; Concatenation; Mitochondrial genomes; Phylogenomics; RADseq; RNAseq; Salamandridae; Species tree; Transcriptomes
 Abstract: The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduces a risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra, a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity. For all six species of the genus Salamandra, and two outgroup species from its sister genus Lyciasalamandra, we used RNA sequencing (RNAseq) and restriction site associated DNA sequencing (RADseq) to obtain data for: (1) 3070 nuclear protein-coding genes from RNAseq; (2) 7440 loci obtained by RADseq; and (3) full mitochondrial genomes. The RNAseq and RADseq data sets retrieved fully congruent topologies when each of them was analyzed in a concatenation approach, with high support for: (1) S. infraimmaculata being sister group to all other Salamandra species; (2) S. algira being sister to S. salamandra; (3) these two species being the sister group to a clade containing S. atra, S. corsica and S. lanzai; and (4) the alpine species S. atra and S. lanzai being sister taxa. The phylogeny inferred from the mitochondrial genome sequences differed from these results, most notably by strongly supporting a clade containing S. atra and S. corsica as sister taxa. A different placement of S. corsica was also retrieved when analysing the RNAseq and RADseq data under species tree approaches. Closer examination of gene trees derived from RNAseq revealed that only a low number of them supported each of the alternative placements of S. atra. Furthermore, gene jackknife support for the S. atra

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Language(s): eng - English
 Dates: 2017-05-312017-02-032017-07-132017-07-142017
 Publication Status: Published in print
 Pages: -
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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: 115 Sequence Number: - Start / End Page: 16 - 26 Identifier: ISSN: 1055-7903
CoNE: /journals/resource/954922650168