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

Autor: Rodríguez A; Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany; Institute of Zoology, Tierärztliche Hochschule Hannover, Bünteweg 17, 30559 Hannover, Germany., Burgon JD; Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK., Lyra M; Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av 24A, N 1515, CEP 13506-900 Rio Claro, SP, Brazil., Irisarri I; Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstr. 10, 78464 Konstanz, Germany., Baurain D; InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Chemin de la Vallée 4, Bât. B22, 4000 Liège, Belgium., Blaustein L; Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel., Göçmen B; Science Faculty, Biology Department, Zoology Section, Ege University, Turkey., Künzel S; Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany., Mable BK; Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK., Nolte AW; Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany; Carl von Ossietzky University Oldenburg, Institute for Biology, Carl von Ossietzky Str. 9-11, 26111 Oldenburg, Germany., Veith M; Biogeography Department, Trier University, 54286 Trier, Germany., Steinfartz S; Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany., Elmer KR; Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK., Philippe H; Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, 2 route du CNRS, 09200 Moulis, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC H3C 3J7, Canada., Vences M; Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany. Electronic address: m.vences@tu-bs.de.
Jazyk: angličtina
Zdroj: Molecular phylogenetics and evolution [Mol Phylogenet Evol] 2017 Oct; Vol. 115, pp. 16-26. Date of Electronic Publication: 2017 Jul 14.
DOI: 10.1016/j.ympev.2017.07.009
Abstrakt: 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 - S. lanzai node stabilized only with very large concatenated data sets. The phylogeny of true salamanders thus provides a compelling example of how classical node support metrics such as bootstrap and Bayesian posterior probability can provide high confidence values in a phylogenomic topology even if the phylogenetic signal for some nodes is spurious, highlighting the importance of complementary approaches such as gene jackknifing. Yet, the general congruence among the topologies recovered from the RNAseq and RADseq data sets increases our confidence in the results, and validates the use of phylotranscriptomic approaches for reconstructing shallow relationships among closely related taxa. We hypothesize that the evolution of Salamandra has been characterized by episodes of introgressive hybridization, which would explain the difficulties of fully reconstructing their evolutionary relationships.
(Copyright © 2017. Published by Elsevier Inc.)
Databáze: MEDLINE
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