Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles

• Published in: Molecular phylogenetics and evolution Vol. 198; p. 108130
• Main Authors: Sherlock, Miranda B., Streicher, Jeffrey W., Gower, David J., Maddock, Simon T., Nussbaum, Ronald A., Oommen, Oommen V., Serra Silva, Ana, Day, Julia J., Wilkinson, Mark
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2024
• Subjects: Amphibians - classification; Amphibians - genetics; Ancient clade; Animals; Caecilian; ddRADseq; Island biogeography; Islands; Phylogenomics; Phylogeny; Phylogeography; Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Seychelles; Seychelles; ddRADseq; Caecilian; Island biogeography; Phylogenomics; Ancient clade
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2024.108130

[Display omitted] •ddRADseq resolves phylogeny of Seychelles caecilians (Amphibia: Gymnophiona).•Permitting individual missing data up to 90 % benefits phylogenetic inference.•Paraphyletic genera support transfer of all Grandisonia species to Hypogeophis.•Phylogeny supports single origin of diminutive, abbreviated caecilians. Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.