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French CM, Berezin CT, Overcast I, Méndez De La Cruz FR, Basu S, Martínez Bernal RL, Murphy RW, Hickerson MJ, Blair C. Forest cover and geographical distance influence fine-scale genetic structure of leaf-toed geckos in the tropical dry forests of western Mexico. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographical distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the Last Glacial Maximum. Landscape genetic analyses suggest that the combination of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) has influenced the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to affect native fauna.
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Affiliation(s)
- Connor M French
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
| | - Casey-Tyler Berezin
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Isaac Overcast
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Institut de Biologie de l’Ecole Normale Superieure , 46 Rue d’Ulm, 75005 Paris , France
- Division of Vertebrate Zoology, American Museum of Natural History , 200 Central Park West, New York, NY 10024 , USA
| | | | - Saptarsi Basu
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
| | | | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum , 100 Queen’s Park, Toronto, ON M5S 2C6 , Canada
| | - Michael J Hickerson
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Christopher Blair
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
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Blair C, Bryson RW, García-Vázquez UO, Nieto-Montes De Oca A, Lazcano D, Mccormack JE, Klicka J. Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.
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Affiliation(s)
- Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, NY, USA
- Biology PhD Program, CUNY Graduate Center, New York, NY, USA
| | - Robert W Bryson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA
| | - Uri O García-Vázquez
- Laboratorio de Sistemática Molecular, Unidad Multidisiplinaria de Investigacion Experimental, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autonoma de México, Ciudad de México, Mexico
| | - Adrián Nieto-Montes De Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autonoma de México, Cd. Universitaria, Ciudad de México, Mexico
| | - David Lazcano
- Laboratorio de Herpetología, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, Nuevo León CP, Mexico
| | - John E Mccormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, USA
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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Ramírez-Reyes T, Barraza-Soltero IK, Nolasco-Luna JR, Flores-Villela O, Escobedo-Galván AH. A new species of leaf-toed gecko (Phyllodactylidae, Phyllodactylus) from María Cleofas Island, Nayarit, Mexico. Zookeys 2021; 1024:117-136. [PMID: 33776523 PMCID: PMC7985131 DOI: 10.3897/zookeys.1024.60473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/05/2021] [Indexed: 01/13/2023] Open
Abstract
We describe a new species of leaf-toed gecko of the genus Phyllodactylus from María Cleofas Island, the smallest island of Tres Marías Archipelago, Nayarit, México. Genomic, phylogenomic, and morphological evidence support that the new species presents a unique combination of diagnostic characters. Morphologically, the new species has a high number of tubercles, head to tail (mean 47), longitudinal ventral scales (mean 61), and third labial-snout scales (mean 26). Gene flow tests revealed the genetic isolation of insular populations from mainland counterparts. In addition, we confirmed the non-monophyly of P. homolepidurus and P. nolascoensis, and we show that the taxon P. t. saxatilis is a complex; therefore, we propose taxonomic changes within the saxatilis clade. The discovery of this new insular endemic species highlights the urgency of continued exploration of the biological diversity of island faunas of Mexico.
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Affiliation(s)
- Tonatiuh Ramírez-Reyes
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, primer piso, Universidad Nacional Autónoma de México, Ciudad Universitaria 3000, Coyoacán, Ciudad de México, México.,Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Ilse K Barraza-Soltero
- Centro Universitario de la Costa, Universidad de Guadalajara, Av. Universidad 203, 48280, Puerto Vallarta, Jalisco, México.,Laboratorio de Ecología del Comportamiento, Centro de Investigaciones Biológicas del Noroeste, S.C., Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, Apdo. Postal 128; La Paz, BCS 23096, México
| | - Jose Rafael Nolasco-Luna
- Centro Universitario de la Costa, Universidad de Guadalajara, Av. Universidad 203, 48280, Puerto Vallarta, Jalisco, México.,Universidad Autónoma de Nayarit, Ciudad de la Cultura " Amado Nervo" s/n, 63155, Tepic, Nayarit, México
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Armando H Escobedo-Galván
- Centro Universitario de la Costa, Universidad de Guadalajara, Av. Universidad 203, 48280, Puerto Vallarta, Jalisco, México
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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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Clause AG, Luna-Reyes R, De Oca ANM. A New Species of Abronia (Squamata: Anguidae) from a Protected Area in Chiapas, Mexico. HERPETOLOGICA 2020. [DOI: 10.1655/herpetologica-d-19-00047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Adam G. Clause
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | - Roberto Luna-Reyes
- Dirección de Gestión, Investigación y Educación Ambiental, Secretaría de Medio Ambiente e Historia Natural, Tuxtla Gutiérrez 29000, Chiapas, México
| | - Adrián Nieto-Montes De Oca
- Laboratorio de Herpetología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, México
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Newton LG, Starrett J, Hendrixson BE, Derkarabetian S, Bond JE. Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex. Mol Ecol 2020; 29:2269-2287. [PMID: 32452095 DOI: 10.1111/mec.15483] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.
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Affiliation(s)
- Lacie G Newton
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | | | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, CA, USA
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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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