Reverse taxonomy of fish-scale geckos (Geckolepis) using shotgun sequencing for museomics-based assignment of historical names to genetic lineages

Abstract

Fish-scale geckos (Geckolepis), endemic to Madagascar and the Comoro Islands, are nocturnal, arboreal lizards with large, imbricate scales that can be shed and regenerated in their entirety, most likely as an antipredator mechanism. Their species-level taxonomy has remained partly unresolved because morphology alone has proven insufficient to reliably assign genetic lineages to scientific names. Here, we use a museomics approach to extract and shotgun-sequence DNA from twelve liquid-preserved historical and mostly name-bearing type specimens of six historical nomina in the genus, and assemble sequences of the mitochondrial genes for 12S rRNA, 16S rRNA, and nd4 for ten of these specimens. Despite relatively low coverage, the assembled sequences robustly placed all these type specimens in a phylogenetic tree with 113 ingroup samples collected across Madagascar. Our results demonstrate the efficiency of this approach to recover mitochondrial evidence for taxonomic purposes, but also show its failure to recover reads matching single-copy nuclear genes. We discuss the promise of a renewed focus on nuclear ribosomal genes as complementary nuclear-encoded DNA barcodes for vertebrates, as we found 18S rRNA sequences to be well-represented among the reads of the historical specimens studied here. Based on evidence from the mitochondrial tree, two nuclear-encoded genes (C-MOS, RAG-1), and morphology, we resurrect G. typica var. modesta Methuen & Hewitt, 1913 as a full species, G. modesta, from north-western Madagascar, confirm the current use of the name G. maculata Peters, 1880 for specimens from northern and eastern Madagascar, of G. polylepis Boettger, 1893 for specimens from western and north-western Madagascar, and of G. typica Grandidier, 1867 for specimens from southern and south-western Madagascar. We also recognize G. typica var. anomala Mocquard, 1902 as a subspecies, G. typica anomala, and confirm G. petiti Angel, 1942 to be a synonym of this subspecies. We also describe two new species, G. bekira sp. nov. and G. spania sp. nov. from northern Madagascar. The new classification provides a robust baseline to identify the remaining taxonomic issues in the genus and tackle them, preferably using genomic approaches which are also promising to better understand the molecular mechanisms of scarless wound healing and skin regeneration in these geckos.