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

Ariel Rodríguez, James D. Burgon, Mariana Lyra, Iker Irisarri, Denis Baurain, Leon Blaustein, Bayram Göçmen, Sven Künzel, Barbara K. Mable, Arne W. Nolte, Michael Veith, Sebastian Steinfartz, Kathryn R. Elmer, Hervé Philippe, Miguel Vences

Research output: Contribution to journalArticlepeer-review

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 - 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.

Original languageEnglish
Pages (from-to)16-26
Number of pages11
JournalMolecular Phylogenetics and Evolution
Volume115
DOIs
StatePublished - Oct 2017

Bibliographical note

Funding Information:
We are grateful to Marion Ballenghien and Nicolas Galtier for locality information on the sample used for their published S. salamandra transcriptome, to Martin Llewellyn for making computing resources available, to Alan Templeton for support with our research on S. infraimmaculata, to Franco Andreone and Philine Werner for help with obtaining crucial samples, and to David Donaire for continued support. We acknowledge the use of the Altamira Supercomputer (IFCA-CSIC), and support of the Alexander von Humboldt Foundation to II and AR, the European Molecular Biology Organization (EMBO) to II, the German Research Foundation (DFG) (STE1130/8-1 and BL 1271/1-1) as part of a German-Israeli project cooperation (DIP) grant to SS, AN and LB, and of the TULIP Laboratory of Excellence (ANR-10-LABX-41) to HP. This research was supported in part by a Natural Environment Research Council PhD studentship NE/L501918/1 (with KRE and BM) and a Systematics Research Fund award from the Linnean Society of London and the Systematics Association to JB. Support was provided by CalculQu?bec (www.calculquebec.ca) and Compute Canada (www.computecanada.ca).

Publisher Copyright:
© 2017

Keywords

  • Amphibia
  • Caudata
  • Concatenation
  • Mitochondrial genomes
  • Phylogenomics
  • RADseq
  • RNAseq
  • Salamandridae
  • Species tree
  • Transcriptomes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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