Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region

• Published in: Molecular phylogenetics and evolution 2024-08, Vol.197, p.108091, Article 108091
• Main Authors: Kotsakiozi, Panayiota, Antoniou, Aglaia, Psonis, Nikolaos, Sagonas, Κostas, Karameta, Emmanouela, Ilgaz, Çetin, Kumlutaş, Yusuf, Avcı, Aziz, Jablonski, Daniel, Darriba, Diego, Stamatakis, Alexandros, Lymberakis, Petros, Poulakakis, Nikos
• Format: Article
• Language: English
• Subjects: Animals; Cryptic species; ddRADseq; DNA, Mitochondrial - genetics; Gekkonidae; Genetic Variation; Genetics, Population; Lizards - classification; Lizards - genetics; Mediterranean Region; Phylogenomics; Phylogeny; Phylogeography; Polymorphism, Single Nucleotide; Population genomics; Sequence Analysis, DNA; SNPs
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2024.108091

[Display omitted] •Cryptic diversity consists of a great obstacle in assessing the current biodiversity crisis and in conservation efforts.•In eastern Mediterranean region recently revealed such a case of hidden diversity in gecko lizards, with the recognition of five Mediodactylus species within what previously thought to be a single species.•Now genomic data enabled us to resolve the phylogenetic relationships among these five lineages and reveal the evolutionary history of this taxon.•Modern species delimitation approaches using genomic data revealed additional hidden diversity, as it seems that three of the five Mediodactylus species are actually species complexes. Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.