Phylogenomic inference of species and subspecies diversity in the Palearctic salamander genus Salamandra

Burgon, J. D. et al. (2021) Phylogenomic inference of species and subspecies diversity in the Palearctic salamander genus Salamandra. Molecular Phylogenetics and Evolution, 157, 107063. (doi: 10.1016/j.ympev.2020.107063) (PMID:33387650)

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Abstract

The salamander genus Salamandra is widespread across Europe, North Africa, and the Near East and is renowned for its conspicuous and polymorphic colouration and diversity of reproductive modes. The phylogenetic relationships within the genus, and especially among the highly polymorphic species S. salamandra, have been very challenging to elucidate, leaving its real evolutionary history and classification at species and subspecies levels a topic of debate and contention. However, the distribution of diversity and species delimitation within the genus are critically important for identifying evolutionarily significant units for conservation and management, especially in light of threats posed by the pathogenic chytrid fungus Batrachochytrium salamandrivorans that is causing massive declines of S. salamandra populations in central Europe. Here, we conducted a phylogenomic analysis from across the taxonomic and geographic breadth of the genus Salamandra in its entire range. Bayesian, maximum likelihood and network-based phylogenetic analyses of up to 4,905 ddRADseq-loci (294,300 nucleotides of sequence) supported the distinctiveness of all currently recognised species (Salamandra algira, S. atra, S. corsica, S. infraimmaculata, S. lanzai, and S. salamandra), and all five species for which we have multiple exemplars were confirmed as monophyletic. Within S. salamandra, two main clades can be distinguished: one clade with the Apenninic subspecies S. s. gigliolii nested within the Iberian S. s. bernardezi/fastuosa; the second clade comprising all other Iberian, Central and East European subspecies. Our analyses revealed that some of the currently recognized subspecies of S. salamandra are paraphyletic and may require taxonomic revision, with the Central- and Eastern-European subspecies all being poorly differentiated in the analysed genomic markers. Salamandra s. longirostris – sometimes considered a separate species – was nested within S. salamandra, consistent with its subspecies status. The relationships identified within and between Salamandra species provide valuable context for future systematic and biogeographic studies, and help elucidate critical evolutionary units for conservation and taxonomy.

Item Type:Articles
Additional Information:This work was funded by a Natural Environment Research Council (NERC) research studentship NE/L501918/1 to JDB with KRE and BKM. Partial funding also came from a Royal Society Research Grant to KRE and a Systematics Research Fund award, from the Linnean Society of London and the Systematics Association, to JDB. GVA is supported by FCT (IF/01425/2014). SS received support by the German Research Foundation (DFG) (STE1130/8-1 and BL 1271/1-1) as part of a German-Israeli project cooperation (DIP) grant. DRV received support by a Spanish Ministerio de Economía y Competitividad and FEDER CGL2017-89898-R (AEI/FEDER, UE) and LIFE18 NATES000121-LIFE DIVAQUA grants.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Elmer, Professor Kathryn and Mable, Professor Barbara and Burgon, James
Creator Roles:
Burgon, J.Methodology, Conceptualization, Investigation, Formal analysis, Writing – original draft
Mable, B.Supervision, Writing – review and editing
Elmer, K.Supervision, Conceptualization, Formal analysis, Writing – original draft
Authors: Burgon, J. D., Vences, M., Steinfartz, S., Bogaerts, S., Bonato, L., Donaire-Barroso, D., Martínez-Solano, I., Velo-Anton, G., Vieites, D. R., Mable, B. K., and Elmer, K. R.
College/School:College of Medical Veterinary and Life Sciences
College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
Journal Name:Molecular Phylogenetics and Evolution
Publisher:Elsevier
ISSN:1055-7903
ISSN (Online):1095-9513
Published Online:31 December 2020
Copyright Holders:Copyright © 2020 Elsevier
First Published:First published in Molecular Phylogenetics and Evolution 157: 107063
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
190635NERC DTG 2013 - 2017Mary Beth KneafseyNatural Environment Research Council (NERC)NE/L501918/1Research and Innovation Services