title: Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity.
abstract: Middle American knob-scaled lizards of the genus Xenosaurus are a unique radiation of viviparous species that are generally characterized by a flattened body shape and a crevice-dwelling ecology. Only eight species of Xenosaurus, one of them with five subspecies (X. grandis), have been formally described. However, species limits within Xenosaurus have never been examined using molecular data, and no complete phylogeny of the genus has been published. Here, we used ddRADseq data from all of the described and potentially undescribed taxa of Xenosaurus to investigate species limits, and to obtain a phylogenetic hypothesis for the genus. We analyzed the data using a variety of phylogenetic models, and were able to reconstruct a well-resolved and generally well-supported phylogeny for this group. We found Xenosaurus to be composed of four major, allopatric clades concordant with geography. The first and second clades that branch off the tree are distributed on the Atlantic slopes of the Sierra Madre Oriental and are composed of X. mendozai, X. platyceps, and X. newmanorum, and X. tzacualtipantecus and an undescribed species from Puebla, respectively. The third clade is distributed from the Atlantic slopes of the Mexican Transvolcanic Belt in west-central Veracruz south to the Pacific slopes of the Sierra Madre del Sur in Guerrero and Oaxaca, and is composed of X. g. grandis, X. rectocollaris, X. phalaroanthereon, X. g. agrenon, X. penai, and four undescribed species from Oaxaca. The last clade is composed of the four taxa that are geographically closest to the Isthmus of Tehuantepec (X. g. arboreus, X. g. rackhami, X. g. sanmartinensis, and an undescribed species from Oaxaca). We also utilized a variety of molecular species delimitation approaches, including analyses with GMYC, PTP, BPP, and BFD∗, which suggested that species diversity in Xenosaurus is at least 30% higher than currently estimated.
authors.affiliation: Laboratorio de Herpetología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, D.F., C.P. 04510, Mexico. Electronic address: anietomontesdeoca@me.com.
authors.forename: Adrián
authors.initials: A
authors.lastname: Nieto-Montes de Oca
authors.affiliation: Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Barley
authors.affiliation: Laboratorio de Herpetología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, D.F., C.P. 04510, Mexico.
authors.forename: Rubi N
authors.initials: RN
authors.lastname: Meza-Lázaro
authors.affiliation: Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Batalla 5 de Mayo s/n, Ejército de Oriente, México, D.F., C.P. 09230, Mexico.
authors.forename: Uri O
authors.initials: UO
authors.lastname: García-Vázquez
authors.affiliation: Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Medellín, Antioquía 050034, Colombia.
authors.forename: Joan G
authors.initials: JG
authors.lastname: Zamora-Abrego
authors.affiliation: Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Thomson
authors.affiliation: Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Leaché
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D044822:Biodiversity; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D008116:Lizards / Q000145:classification* / Q000235:genetics; D008800:Mexico; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Middle America; Phylogenomics; Species delimitation; Xenosaurus; ddRADseq