Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog ( Sarcohyla ; Hylidae)

• Published in: PeerJ (San Francisco, CA) Vol. 6; p. e6045
• Main Authors: Zarza, Eugenia, Connors, Elizabeth M, Maley, James M, Tsai, Whitney L E, Heimes, Peter, Kaplan, Moises, McCormack, John E
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 11.12.2018; PeerJ, Inc; PeerJ Inc
• Subjects: Amphibians; Biodiversity; Biogeography; Bioinformatics; Biological research; Deoxyribonucleic acid; Dispersal; DNA; DNA sequencing; Endemic species; Genetic analysis; Genetic aspects; Genetic research; Genomes; Genomic analysis; Genomics; Hylidae; Hylinae; Identification and classification; Methods; Mitochondrial DNA; New species; Phenotypes; Phylogenetics; Phylogeny; Phylogeography; Physical characteristics; Population genetics; Reptiles & amphibians; Retirement benefits; Single-nucleotide polymorphism; Species limits; Systematic biology; Systematics; Zoology; Mexico; United States > US; Systematics; Genomics; Phylogeography; Phylogenetics; Mexico; Hylinae; Species limits; Biodiversity; Population genetics
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.6045

Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs ( , Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described as . Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgent goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature in and may have acted as a dispersal corridor for to spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species.