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

• Published in: Molecular phylogenetics and evolution Vol. 157; p. 107063
• Main Authors: Burgon, James D., Vences, Miguel, Steinfartz, Sebastian, Bogaerts, Sergé, Bonato, Lucio, Donaire-Barroso, David, Martínez-Solano, Iñigo, Velo-Antón, Guillermo, Vieites, David R., Mable, Barbara K., Elmer, Kathryn R.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-04-2021
• Subjects: Amphibia; Animals; Bayes Theorem; Biodiversity; Caudata; ddRADseq; Genotype; Geography; Phylogeny; Principal Component Analysis; Salamandra salamandra; Species Specificity; Subspecies; Urodela - classification; Urodela - genetics; Western Palearctic; Amphibia; ddRADseq; Salamandra salamandra; Western Palearctic; Caudata; Subspecies
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2020.107063

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•ddRADseq clarifies relationships among 23 of the 25 recognized Salamandra subspecies.•S. salamandra longirostris is placed in a clade with other Iberian subspecies.•The Italian S. s. gigliolii is phylogenetically nested within the Iberian subspecies fastuosa and bernardezi.•Highest genomic diversity of S. salamandra is found in the Iberian Peninsula.•Weak genomic differentiation among the Central and Eastern European subspecies of S. salamandra.
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 in 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 4905 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; and a 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 at 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.