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Castiglia R, Flores-Villela OA, Bezerra AMR, Gornung E, Annesi F, Muñoz-Alonso LA, Solano E. Detection of cryptic diversity in lizards (Squamata) from two Biosphere Reserves in Mesoamerica. COMPARATIVE CYTOGENETICS 2020; 14:613-638. [PMID: 33384855 PMCID: PMC7772285 DOI: 10.3897/compcytogen.v14i4.57765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
A combined approach based on karyology and DNA taxonomy allowed us to characterize the taxonomic peculiarities in 10 Mesoamerican lizard species, belonging to six genera and five families, inhabiting two Biosphere Reserve in Chiapas, Mexico: La Sepultura Biosphere Reserve, and Montes Azules Biosphere. The karyotypes of four species, Phyllodactylus sp. 3 (P. tuberculosus species group) (2n = 38), Holcosus festivus (Lichtenstein et von Martens, 1856) (2n = 50), Anolis lemurinus Cope, 1861 (2n = 40), and A. uniformis Cope, 1885 (2n = 29-30) are described for the first time, the last one showing a particular X1X1X2X2/X1X2Y condition. In Aspidoscelis deppii (Wiegmann, 1834) (2n = 50) and Anolis capito Peters, 1863 (2n = 42), we found a different karyotype from the ones previously reported for these species. Moreover, in A. capito, the cytogenetic observation is concurrent with a considerable genetic divergence (9%) at the studied mtDNA marker (MT-ND2), which is indicative of a putative new cryptic species. The skink Scincella cherriei (Cope, 1893), showed high values of genetic divergence (5.2% at 16S gene) between the specimens from Montes Azules and those from Costa Rica and Nicaragua, comparable to the values typical of sister species in skinks. A lower level of genetic divergence, compatible with an intraspecific phylogeographic structure, has been identified in Lepidophyma flavimaculatum Duméril, 1851. These new data identify taxa that urgently require more in-depth taxonomic studies especially in these areas where habitat alteration is proceeding at an alarming rate.
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Affiliation(s)
- Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
| | - Oscar Alberto Flores-Villela
- Museo de Zoologia Fac. de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-399, Mexico D.F. 04510, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Alexandra M. R. Bezerra
- Mastozoologia/COZOO, Museu Paraense Emilio Goeldi, Campus de Pesquisa, Av. Perimetral 1901, CEP 66077-830, Belém, PA, BrazilMuseu Paraense Emilio GoeldiBelémBrazil
| | - Ekaterina Gornung
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
| | - Flavia Annesi
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
| | - Luis Antonio Muñoz-Alonso
- El Colegio de la Frontera Sur. Conservación de las Biodiversidad. Carretera Panamericana y Periférico Sur s/n. C.P. 29290, San Cristóbal de las Casas, Chiapas, MéxicoEl Colegio de la Frontera Sur. Conservación de las BiodiversidadSan Cristóbal de las CasasMexico
| | - Emanuela Solano
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma ‘La Sapienza’, via A. Borelli 50, CAP 00151, Rome, ItalyUniversità di Roma ‘La Sapienza’RomeItaly
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Ramírez-Reyes T, Blair C, Flores-Villela O, Piñero D, Lathrop A, Murphy R. Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico. Mol Phylogenet Evol 2020; 150:106880. [PMID: 32512192 DOI: 10.1016/j.ympev.2020.106880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using two approaches: supermatrix and coalescent-based inference. All topologies depict three, mutually exclusive major clades. Clade I comprises P. bordai and all species closer to P. bordai than to any other Phyllodactylus. Clade II comprises P. nocticolus and all species closer to P. nocticolus than to any other Phyllodactylus. Clade III comprises P. tuberculosus and all species closer to P. tuberculosus than to any other Phyllodactylus. Analyses estimate the age for the most recent common ancestor of Phyllodactylus in the Eocene (~43 mya), and the ancestors of each major clade date to the Eocene-Oligocene transition (32-36 mya). This group includes one late-Eocene lineage (P. bordai), Oligocene lineages (P. paucituberculatus, P. delcampi), but also topological patterns that indicate a recent radiation occurred during the Pleistocene on islands in the Gulf of California. The wide spatial and temporal scale indicates a complex and unique biogeographic history for each major clade. The 33 species delimited by BPP and stepping-stone BFD*coalescent based genomic approaches reflect this history. This diversity delimited for Mexican leaf-toed geckos demonstrates a vast underestimation in the number of species based on morphological data alone.
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Affiliation(s)
- Tonatiuh Ramírez-Reyes
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510 Ciudad de México, Mexico; Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510 Ciudad de México, Mexico; Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, 04510 Ciudad de México, Mexico.
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA; Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, 04510 Ciudad de México, Mexico
| | - Amy Lathrop
- Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, Toronto, Ontario, Canada
| | - Robert Murphy
- Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, Toronto, Ontario, Canada; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
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Molecular systematics, species delimitation and diversification patterns of the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico. Mol Phylogenet Evol 2017; 115:82-94. [PMID: 28739370 DOI: 10.1016/j.ympev.2017.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 11/21/2022]
Abstract
The description of cryptic gecko species worldwide has revealed both that many putative species are, in fact, conformed by a complex of morphologically conserved species that are genetically distinct and highly divergent, and that gecko species diversity could be underestimated. The taxonomy and species delimitation of geckos belonging to the genus Phyllodactylus is still controversial, 16 of which are distributed in Mexico and 13 are endemic. Although the large morphological variation shown by the Phyllodactylus species from Mexico has been amply documented, little is known about their genetic diversity and evolutionary relationships, and much less regarding cryptic speciation. Here, we included the most comprehensive sampling of populations and species of the Phyllodactylus lanei complex distributed in Mexico, and applied an analytical approach that included probabilistic phylogenetic analyses, jointly with species delimitation methods and Bayesian putative species validation analysis. Our results suggest the existence of 10 lineages within the complex, supporting the existence of cryptic species, and in great contrast with the current taxonomic proposal that includes only four subspecies. The most recent common ancestor (MRCA) for the P. lanei clade originated on the Early Eocene (∼54Mya), along the southern coasts of Mexico, followed by the highest diversification of the complex MRCA during the Eocene (34-56Mya). Lineages subsequently dispersed and diversified towards the northwest, and the diversification process ended with the most recent lineages inhabiting two islands on the coasts of Nayarit (Miocene; 5.5-23Mya). Our results highlight three vicariant events associated with the evolution of the lineages, two of them intimately related to the formation of the Sierra Madre del Sur and the Transmexican Volcanic Belt mountain ranges, main geographic barriers that isolated and facilitated the divergence and speciation in this group of geckos. Finally, we propose that there are 10 species in the P. lanei complex, from which four represent taxonomic changes and six are new species and require a formal description. We acknowledge that more analyses, including a detailed evaluation of morphological characters and use of more unlinked nuclear loci with enough variability, are needed to further support their taxonomic description.
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Blair C, Jiménez Arcos VH, de la Cruz FRM, Murphy RW. Historical and contemporary demography of leaf-toed geckos (Phyllodactylidae: Phyllodactylus tuberculosus saxatilis) in the Mexican dry forest. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0668-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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