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Hurtado-Gómez JP, Vargas-Ramírez M, Iverson JB, Joyce WG, McCranie JR, Paetzold C, Fritz U. Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae). Mol Phylogenet Evol 2024; 197:108083. [PMID: 38679303 DOI: 10.1016/j.ympev.2024.108083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/02/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
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Affiliation(s)
| | - Mario Vargas-Ramírez
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, IN 47374, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, 1700 Fribourg, Switzerland
| | - James R McCranie
- Smithsonian Research Associate, 10770 SW 164th Street, Miami, FL 33157, USA
| | - Claudia Paetzold
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany.
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2
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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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Muñoz-Mora VH, Suárez-Atilano M, Maltagliati F, Ramírez-Corona F, Carbajal-Saucedo A, Percino-Daniel R, Langeneck J, D’Addario M, Sunny A. A tale about vipers’ tails: phylogeography of black-tailed rattlesnakes. HERPETOZOA 2022. [DOI: 10.3897/herpetozoa.35.e84297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The phylogenetic relationships among black-tailed rattlesnakes remain poorly understood and some authors indicated that the diversity of this group has been underestimated and additional analyses are required to clarify the biogeographic patterns throughout its distribution in Mexico. Therefore, the aim of this study was to elucidate the phylogenetic relationships among black-tailed rattlesnakes across their range, identifying relative divergence times among the main clades and reconstructing the biogeographical history of the group. Three partial mitochondrial genes (ND4, cytb and ATPase6) and one nuclear gene (RAG1) were sequenced to infer the phylogenetic relationships, through the maximum likelihood and Bayesian inference-based methods; demographic history reconstruction was investigated through Bayesian Skyline plot analysis and the ancestral area reconstruction was carried out considering a Bayesian framework. We found strong evidence that the black-tailed rattlesnakes’ group is composed of six clades, which is in agreement with subspecies previously reported. Divergence time estimation indicated that the origin of the C. molossus group could be traced to the middle of the Miocene (~7.71 Mya). Ancestral area reconstruction indicated that early divergence events occurred in Central Mexico, probably related to the geological dynamics of the Trans-Mexican Volcanic Belt. The lineage C. m. oaxacus is the basal member of the C. molossus group. Furthermore, the combination of geological events and changes in Quaternary vegetation may have contributed to the divergence of C. molossus clades. Our results suggest several clades within C. molossus complex could be potentially recognized as separate species.
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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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García‐Sotelo UA, García‐Vázquez UO, Espinosa D. Historical biogeography of the genus Rhadinaea (Squamata: Dipsadinae). Ecol Evol 2021; 11:12413-12428. [PMID: 34594509 PMCID: PMC8462180 DOI: 10.1002/ece3.7988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/31/2021] [Accepted: 06/28/2021] [Indexed: 11/12/2022] Open
Abstract
Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as "Eastern" and "Southern". These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans-Mexican Volcanic Belt and Chiapan-Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans-Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.
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Affiliation(s)
- Uriel A. García‐Sotelo
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Uri O. García‐Vázquez
- Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - David Espinosa
- Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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Castillo-Chora VDJ, Sánchez-González LA, Mastretta-Yanes A, Prieto-Torres DA, Navarro-Sigüenza AG. Insights into the importance of areas of climatic stability in the evolution and maintenance of avian diversity in the Mesoamerican dry forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.
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Affiliation(s)
- Vicente De J Castillo-Chora
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México
| | - Luis A Sánchez-González
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Alicia Mastretta-Yanes
- CONACYT—CONABIO, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Liga Periférico-Insurgentes Sur No. 4903, Parques del Pedregal, Tlalpan, Mexico City, México
| | - David A Prieto-Torres
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
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Graham MR, Santibáñez‐López CE, Derkarabetian S, Hendrixson BE. Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq. Mol Ecol 2020; 29:3684-3701. [DOI: 10.1111/mec.15588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | | | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology Museum of Comparative Zoology Harvard University Cambridge MA USA
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Leavitt DH, Hollingsworth BD, Fisher RN, Reeder TW. Introgression obscures lineage boundaries and phylogeographic history in the western banded gecko, Coleonyx variegatus (Squamata: Eublepharidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe geomorphological formation of the Baja California peninsula and the Gulf of California is a principal driver of diversification for the reptiles of North America’s warm deserts. The western banded gecko, Coleonyx variegatus, is distributed throughout the Mojave, Sonoran and Peninsular deserts. In this study we use multilocus sequence data to address deep phylogeographic structure within C. variegatus. Analyses of mtDNA data recover six divergent clades throughout the range of C. variegatus. Topology of the mtDNA gene tree suggests separate origins of peninsular populations with an older lineage in the south and a younger one in the north. In contrast, analyses of multilocus nuclear data provide support for four lineages, corresponding to the subspecies C. v. abbotti, C. v. peninsularis, C. v. sonoriensis and C. v. variegatus. Phylogenetic analyses of the nuclear data recover C. v. abbotti and C. v. peninsularis as a clade, indicating a single origin of the peninsular populations. Discordance between the nuclear and mtDNA data is largely the result of repeated episodes of mtDNA introgression that have obscured both lineage boundaries and biogeographic history. Dating analyses of the combined nuclear and mtDNA data suggest that the peninsular clade diverged from the continental group in the Late Miocene.
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Affiliation(s)
| | - Bradford D Hollingsworth
- San Diego State University, San Diego, CA, USA
- San Diego Natural History Museum, El Prado, San Diego, CA, USA
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Venomics of the Central American Lyre Snake Trimorphodon quadruplex (Colubridae: Smith, 1941) from Costa Rica. J Proteomics 2020; 220:103778. [DOI: 10.1016/j.jprot.2020.103778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
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Rocha-Méndez A, Sánchez-González LA, González C, Navarro-Sigüenza AG. The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico. BMC Evol Biol 2019; 19:237. [PMID: 31888449 PMCID: PMC6937948 DOI: 10.1186/s12862-019-1564-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/15/2019] [Indexed: 11/30/2022] Open
Abstract
Background Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. Results We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. Conclusions Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.
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Affiliation(s)
- Alberto Rocha-Méndez
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico. .,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico.
| | - Luis A Sánchez-González
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico
| | - Clementina González
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510, Mexico City, Mexico.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
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Ramírez‐Barrera SM, Velasco JA, Orozco‐Téllez TM, Vázquez‐López AM, Hernández‐Baños BE. What drives genetic and phenotypic divergence in the Red-crowned Ant tanager ( Habia rubica, Aves: Cardinalidae), a polytypic species? Ecol Evol 2019; 9:12339-12352. [PMID: 31832165 PMCID: PMC6854386 DOI: 10.1002/ece3.5742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 09/15/2019] [Indexed: 01/28/2023] Open
Abstract
AIM The effects of geographic and environmental variables on patterns of genetic and phenotypic differentiation have been thoroughly studied. Ecological speciation involves reproductive isolation due to divergent natural selection that can result in a positive correlation between genetic divergence and adaptive phenotypic divergence (isolation by adaptation, IBA). If the phenotypic target of selection is unknown or not easily measured, environmental variation can be used as a proxy, expecting positive correlation between genetic and environmental distances, independent of geographic distances (isolation by environment, IBE). The null model is that the amount of gene flow between populations decreases as the geographic distance between them increases, and genetic divergence is due simply to the neutral effects of genetic drift (isolation by distance, IBD). However, since phenotypic differentiation in natural populations may be autocorrelated with geographic distance, it is often difficult to distinguish IBA from the neutral expectation of IBD. In this work, we test hypotheses of IBA, IBE, and IBD in the Red-crowned Ant tanager (Habia rubica). LOCATION Mesoamerica (Mexico-Central America) and South America. TAXON Habia rubica (Aves: Cardinalidae). METHODS We compiled genetic data, coloration, and morphometric data from specimens from collections in Mexico and the United States. We used the Multiple Matrix Regression with Randomization (MMRR) approach to evaluate the influence of geographic and environmental distances on genetic and phenotypic differentiation of H. rubica at both phylogroup and population levels. RESULTS Our results provide strong evidence that geographic distance is the main driver of genetic variation in H. rubica. We did not find evidence that climate variation is driving population differentiation in this species across a widespread geographic region. MAIN CONCLUSIONS Our data point to geographic isolation as the main factor structuring genetic variation within populations of H. rubica and suggest that climate is not playing a major role in genetic differentiation within this species.
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Affiliation(s)
- Sandra M. Ramírez‐Barrera
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Julián A. Velasco
- Centro de Ciencias de la AtmósferaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Tania M. Orozco‐Téllez
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Alma M. Vázquez‐López
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Blanca E. Hernández‐Baños
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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12
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Ballesteros-Nova NE, Pérez-Rodríguez R, Beltrán-López RG, Domínguez-Domínguez O. Genetic differentiation in the southern population of the Fathead Minnow Pimephales promelas Rafinesque (Actinopterygii: Cyprinidae). PeerJ 2019; 7:e6224. [PMID: 31106042 PMCID: PMC6497047 DOI: 10.7717/peerj.6224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 12/05/2018] [Indexed: 12/27/2022] Open
Abstract
The North American cyprinid Pimephales promelas is a species with a wide distribution range, occurring in distinct hydrographic basins in Mexico, Canada, and the United States. Previous morphological and meristic analyses of P. promelas concluded that at least three subspecies exist in the midwestern and northeast region of the United States. No studies have been carried out on the Mexican population of P. promelas, but the findings of cryptic diversity in United States populations of this species, as well as in other codistributed fish species in Mexico could be an indication that Mexican populations of P. promelas consist of cryptic species. Using the mitochondrial gene cyt b and the first intron of the S7 ribosomal protein-coding nuclear gene we carried out phylogenetic and phylogeographic analyses of populations of P. promelas across its distribution range in northwestern Mexico. Using this information were analyzed the structure and differentiation level between populations of P. promelas from distinct river basins in the region in identifying cryptic diversity. Twenty-four sequences were obtained for cyt b, and 30 for S7, which included the two heterozygous alleles. The results revealed the existence of four well-differentiated lineages: (1) Yaqui in the Pacific slope; (2) Santa Maria, and (3) Casas Grandes in the Guzman Basin; and (4) Nazas+Conchos in Chihuahua state. This challenges the current taxonomy of P. promelas. Differences in the relationships between markers and the small sample size for the Santa Maria population (n = 1), indicate that our results must be corroborated with more data and morphological analyses. Biogeographic analysis of these findings suggest that the evolutionary history of P. promelas is associated with the fragmentation of the ancestral Rio Grande river system since Miocene in northwestern Mexico consistent with findings for codistributed fish species.
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Affiliation(s)
- Nayarit E Ballesteros-Nova
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.,Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
| | - Rosa G Beltrán-López
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.,Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.,Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
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13
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Zarza E, Reynoso VH, Faria CMA, Emerson BC. Introgressive hybridization in a Spiny-Tailed Iguana, Ctenosaura pectinata, and its implications for taxonomy and conservation. PeerJ 2019; 7:e6744. [PMID: 31065455 PMCID: PMC6485205 DOI: 10.7717/peerj.6744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
Introgression, the transmission of genetic material of one taxon into another through hybridization, can have various evolutionary outcomes. Previous studies have detected signs of introgression between western populations of the Mexican endemic and threatened spiny-tailed iguana, Ctenosaura pectinata. However, the extent of this phenomenon along the geographic distribution of the species is unknown. Here, we use multilocus data together with detailed geographic sampling to (1) define genotypic clusters within C. pectinata; (2) evaluate geographic concordance between maternally and biparentally inherited markers; (3) examine levels of introgression between genotypic clusters, and (4) suggest taxonomic modifications in light of this information. Applying clustering methods to genotypes of 341 individuals from 49 localities of C. pectinata and the closely related C. acanthura, we inferred the existence of five genotypic clusters. Contact zones between genotypic clusters with signatures of interbreeding were detected, showing different levels of geographic discordance with mtDNA lineages. In northern localities, mtDNA and microsatellites exhibit concordant distributions, supporting the resurrection of C. brachylopha. Similar concordance is observed along the distribution of C. acanthura, confirming its unique taxonomic identity. Genetic and geographic concordance is also observed for populations within southwestern Mexico, where the recognition of a new species awaits in depth taxonomic revision. In contrast, in western localities a striking pattern of discordance was detected where up to six mtDNA lineages co-occur with only two genotypic clusters. Given that the type specimen originated from this area, we suggest that individuals from western Mexico keep the name C. pectinata. Our results have profound implications for conservation, management, and forensics of Mexican iguanas.
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Affiliation(s)
- Eugenia Zarza
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Grupo Académico de Biotecnología Ambiental, El Colegio de la Frontera Sur, Unidad Tapachula, Tapachula, Chiapas, Mexico.,CONACYT, Ciudad de México, Mexico
| | - Víctor H Reynoso
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Christiana M A Faria
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Current Affiliation: Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, Fortaleza, Ceará, Brasil
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, Spain
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14
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Ornelas JF, García JM, Ortiz-Rodriguez AE, Licona-Vera Y, Gándara E, Molina-Freaner F, Vásquez-Aguilar AA. Tracking Host Trees: The Phylogeography of Endemic Psittacanthus sonorae (Loranthaceae) Mistletoe in the Sonoran Desert. J Hered 2019; 110:229-246. [PMID: 30496534 DOI: 10.1093/jhered/esy065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
The host dependence of mistletoes suggests that they track the distributions of their hosts. However, the factors that determine the geographic distribution of mistletoes are not well understood. In this study, the phylogeography of Psittacanthus sonorae was reconstructed by sequencing one nuclear (ITS) and two plastid (trnL-F and atpB-rbcL) regions of 148 plants from populations separated by the Sea of Cortez. Divergence time and gene flow were estimated to gain insight into the historical demography and geographic structuring of genetic variation. We also described and mapped the spatial distribution of suitable habitat occupied by P. sonorae and its most common host Bursera microphylla in the Sonoran Desert, along with their responses to Quaternary climate fluctuations using environmental data and ecological niche modeling (ENM). We detected environmental and genetic differentiation between the peninsular and continental P. sonorae populations. Population divergence occurred during the Pleistocene, around the time of the Last Glacial Maximum. No signals of population growth were detected, with net gene flow moving from the continent to the peninsula. ENM models indicate decoupled responses by the mistletoe and its main host to past climate changes. For the Last Interglacial to the present, most models produce only partial areas of overlap on both the peninsula and the continent. Our results support a scenario of Late-Pleistocene isolation and divergence with asymmetrical gene flow between peninsular and continental P. sonorae populations. Continental populations migrated to the peninsula and the spatial isolation probably produced genetic differentiation under different environmental conditions.
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Affiliation(s)
- Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - José Manuel García
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Andrés E Ortiz-Rodriguez
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico.,Instituto de Investigaciones Forestales, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Yuyini Licona-Vera
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Etelvina Gándara
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico.,Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Francisco Molina-Freaner
- Instituto de Ecología e Instituto de Geología, Universidad Nacional Autónoma de México (UNAM), Estación Regional del Noroeste, Hermosillo, Sonora, Mexico
| | - Antonio Acini Vásquez-Aguilar
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
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15
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Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae). Mol Phylogenet Evol 2018; 129:214-225. [PMID: 30189319 DOI: 10.1016/j.ympev.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022]
Abstract
Accurate representation of lineage diversity through complete taxon sampling is crucial to understanding the evolution of biodiversity, particularly when using molecular phylogenetics to estimate evolutionary relationships. In this interest, taxonomic diversity is often used as a proxy for lineage diversity even though the two concepts are not synonymous. We explore this within the snake tribe Lampropeltini which includes some of the most conspicuous and heavily studied snakes in North America. Both the taxonomy and hypothesized relationships within this tribe have been in flux. The number of species has increased from 23 to 51 over the last thirty years, predominately within three of the nine genera (Lampropeltis, Pantherophis, Pituophis). The remaining six depauperate genera (Arizona, Bogertophis, Cemophora, Pseudelaphe, Rhinocheilus, and Senticolis) have been poorly represented in phylogenetic studies. To estimate evolutionary relationships and determine if the dichotomy in depauperate and speciose genera within Lampropeltini is a function of taxon sampling or truly represents the lineage diversity, we estimated the phylogeny of this group using nuclear and mitochondrial loci in a concatenated and coalescent framework with the largest sampling of the six depauperate genera to date. In addition, we estimated the divergence dates among the genera to assess whether the instability of Lampropeltini phylogenetic relationships is due to an adaptive radiation. While some nodes still remain unresolved, the generic-level relationships we recovered agree with those of a recent next-generation study that used a much larger set of loci for fewer individuals. We also tested two putative species, Arizona pacata and Pseudelaphe phaescens, for the first time phylogenetically and find evidence that they are distinct lineages. Overall, we find that the taxonomic and genetic diversity are not correlated in Lampropeltini and that representing putative diversity in phylogenies will lead to a better estimate of evolutionary histories, especially in groups with complex radiations.
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16
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Ruiz-Vega ML, Hernández-Canchola G, León-Paniagua L. Molecular systematics and phylogeography of the endemic Osgood's deermouse Osgoodomys banderanus (Rodentia: Cricetidae) in the lowlands of western Mexico. Mol Phylogenet Evol 2018; 127:867-877. [PMID: 29958981 DOI: 10.1016/j.ympev.2018.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/26/2022]
Abstract
Osgoodomys banderanus is a recognized and endemic rodent species of western Mexico, an area known for its high biodiversity and number of endemisms. Phylogeographical relationships within this taxon were analyzed based on mitochondrial (ND3, tRNA-Arginine, ND4L and partial ND4) and nuclear (GHR) nucleotide sequences. We obtained a total of 112 samples from 22 localities, covering the complete distribution of the species. Phylogenetic analyses using Maximum Likelihood and Bayesian inference confirmed that Osgoodomys is a monophyletic group. In addition, phylogenetic and phylogeographic analyses detected three major clades, which do not coincide with the recognized subspecies of O. banderanus. The genetic lineages detected are the western clade (Nayarit, Jalisco and northern Colima), the central clade (Colima, Michoacán, and northern Guerrero) and the eastern clade (central and southern Guerrero). Genetic distances among clades (5-9%) and nucleotide substitutions (30-88) among haplogroups were high, especially in the southern group. Mountain ranges such as the Transmexican Volcanic Belt and the Sierra Madre del Sur, as well as the Balsas River act as geographical barriers for Osgoodomys. Our results suggest the presence of three independent species, which need to be characterized morphologically to confirm our hypothesis.
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Affiliation(s)
- M Laura Ruiz-Vega
- Museo de Zoología - Mastozoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
| | - Giovani Hernández-Canchola
- Museo de Zoología - Mastozoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
| | - Livia León-Paniagua
- Museo de Zoología - Mastozoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
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17
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Species limits in the Morelet’s Alligator lizard (Anguidae: Gerrhonotinae). Mol Phylogenet Evol 2018; 120:16-27. [DOI: 10.1016/j.ympev.2017.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 09/21/2017] [Accepted: 11/27/2017] [Indexed: 11/22/2022]
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18
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Arcangeli J, Light JE, Cervantes FA. Molecular and morphological evidence of the diversification in the gray mouse opossum, Tlacuatzin canescens (Didelphimorphia), with description of a new species. J Mammal 2018. [DOI: 10.1093/jmammal/gyx173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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20
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Graham MR, Wood DA, Henault JA, Valois ZJ, Cushing PE. Ancient lakes, Pleistocene climates and river avulsions structure the phylogeography of a large but little-known rock scorpion from the Mojave and Sonoran deserts. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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21
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Gámez N, Nihei SS, Scheinvar E, Morrone JJ. A temporally dynamic approach for cladistic biogeography and the processes underlying the biogeographic patterns of North American deserts. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Niza Gámez
- Museo de Zoología ‘Alfonso L. Herrera’; Departamento de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México (UNAM); Mexico City Mexico
| | - Silvio S. Nihei
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Cidade Universitária; São Paulo SP Brazil
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México (UNAM); Mexico City Mexico
| | - Juan J. Morrone
- Museo de Zoología ‘Alfonso L. Herrera’; Departamento de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México (UNAM); Mexico City Mexico
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22
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Light JE, Ostroff MO, Hafner DJ. Phylogeographic assessment of the northern pygmy mouse, Baiomys taylori. J Mammal 2016. [DOI: 10.1093/jmammal/gyw065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The northern pygmy mouse, Baiomys taylori, occurs throughout the Trans-Mexican Volcanic Belt and southern Altiplano of central Mexico and extends northward in 3 projections into northern Mexico and the United States. We used mitochondrial DNA (from the cytochrome-b and NADH dehydrogenase 2 genes) and morphological data to assess diversity within B. taylori across its geographic range in relation to recognized subspecies and putative physiographic filter-barriers. Our results indicate 5 distinct mitochondrial clades despite little morphological variation across the species’ geographic range. The Sierra Madre Oriental and Sierra Madre Occidental separate clades representing the eastern (Gulf coastal lowlands), central (Altiplano), and Pacific coastal lowlands, which appear to be divided into 3 major mitochondrial clades. Based on a preliminary analysis of cranial morphology, we are able to reject the Balcones Escarpment of Texas as an impediment to the well-documented recent northern expansion of the species, while we are unable to reject a causal role of filter-barriers elsewhere in subspecific differentiation. Revision of subspecific taxonomy must await further genetic sampling, particularly along the western and southeastern portions of the species’ distribution.
El ratón pigmeo norteño, Baiomys taylori, se distribuye a través del Eje Volcánico Transmexicano y la parte sur del Altiplano del centro de México y se extiende hacia el norte de México y los Estados Unidos en tres direcciones. Utilizamos ADN mitocondrial (del citocromo-b y del gen NADH deshidrogenasa) y datos morfológicos para evaluar la diversidad dentro de B. taylori a través de su rango geográfico en relación con las subespecies reconocidas y las supuestas barreras-filtro fisiográficas. Nuestros resultados indican 5 clados mitocondriales distintos a pesar de la escasa variación morfológica a lo largo de su rango geográfico. La Sierra Madre Oriental y la Sierra Madre Occidental separan los clados representantes de las tierras bajas del este (tierras bajas del Golfo), del centro (Altiplano), y las tierras bajas del Pacífico, que parecen estar divididas en 3 clados mitocondriales principales. Basados en un análisis preliminar de la morfología craneal, pudimos rechazar el Escarpe de Balcones de Texas como un impedimento a la bien documentada expansión norteña de la especie, mientras que no fue posible rechazar el rol causal de las otras barreras-filtro en la diferenciación subespecífica. La revisión de la taxonomía subespecífica deberá esperar un mayor muestreo genético, en particular a lo largo de las porciones oeste y sureste de la distribución de la especie.
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23
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Rovito SM, Parra-Olea G. Neotropical Plethodontid Biogeography: Insights from Molecular Phylogenetics. COPEIA 2016. [DOI: 10.1643/ch-14-190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Williford D, Deyoung RW, Honeycutt RL, Brennan LA, Hernández F. Phylogeography of the bobwhite (Colinus) quails. WILDLIFE MONOGRAPHS 2015. [DOI: 10.1002/wmon.1017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Randy W. Deyoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Rodney L. Honeycutt
- Natural Science Division; Pepperdine University, 24255 Pacific Coast Highway; Malibu CA 90263 USA
| | - Leonard A. Brennan
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Fidel Hernández
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
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25
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Mott BM, Gadau J, Anderson KE. Phylogeography of Pogonomyrmex barbatus and P. rugosus harvester ants with genetic and environmental caste determination. Ecol Evol 2015; 5:2798-826. [PMID: 26306168 PMCID: PMC4541987 DOI: 10.1002/ece3.1507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 11/11/2022] Open
Abstract
We present a phylogeographic study of at least six reproductively isolated lineages of new world harvester ants within the Pogonomyrmex barbatus and P. rugosus species group. The genetic and geographic relationships within this clade are complex: Four of the identified lineages show genetic caste determination (GCD) and are divided into two pairs. Each pair has evolved under a mutualistic system that necessitates sympatry. These paired lineages are dependent upon one another because their GCD requires interlineage matings for the production of F1 hybrid workers, and intralineage matings are required to produce queens. This GCD system maintains genetic isolation among these interdependent lineages, while simultaneously requiring co-expansion and emigration as their distributions have changed over time. It has also been demonstrated that three of these four GCD lineages have undergone historical hybridization, but the narrower sampling range of previous studies has left questions on the hybrid parentage, breadth, and age of these groups. Thus, reconstructing the phylogenetic and geographic history of this group allows us to evaluate past insights and hypotheses and to plan future inquiries in a more complete historical biogeographic context. Using mitochondrial DNA sequences sampled across most of the morphospecies' ranges in the U.S.A. and Mexico, we conducted a detailed phylogeographic study. Remarkably, our results indicate that one of the GCD lineage pairs has experienced a dramatic range expansion, despite the genetic load and fitness costs of the GCD system. Our analyses also reveal a complex pattern of vicariance and dispersal in Pogonomyrmex harvester ants that is largely concordant with models of late Miocene, Pliocene, and Pleistocene range shifts among various arid-adapted taxa in North America.
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Affiliation(s)
- Brendon M Mott
- USDA-ARS Carl Hayden Bee Research CenterTucson, Arizona, 85719
- School of Life Sciences, Arizona State UniversityTempe, Arizona, 85287
| | - Jürgen Gadau
- School of Life Sciences, Arizona State UniversityTempe, Arizona, 85287
| | - Kirk E Anderson
- USDA-ARS Carl Hayden Bee Research CenterTucson, Arizona, 85719
- Center for Insect Science, University of ArizonaTucson, Arizona, 85721
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26
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Ruane S, Torres-Carvajal O, Burbrink FT. Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis). PLoS One 2015; 10:e0128543. [PMID: 26083467 PMCID: PMC4470684 DOI: 10.1371/journal.pone.0128543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/28/2015] [Indexed: 01/02/2023] Open
Abstract
The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene.
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Affiliation(s)
- Sara Ruane
- Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY, 10314, United States of America
- The Graduate Center, City University of New York, 365 5 Avenue, New York, NY, 10016, United States of America
- * E-mail:
| | - Omar Torres-Carvajal
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Frank T. Burbrink
- Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY, 10314, United States of America
- The Graduate Center, City University of New York, 365 5 Avenue, New York, NY, 10016, United States of America
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27
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Grummer JA, Calderón-Espinosa ML, Nieto-Montes de Oca A, Smith EN, Méndez-de la Cruz FR, Leaché AD. Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands. Mol Ecol 2015; 24:1523-42. [PMID: 25712551 DOI: 10.1111/mec.13122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 02/06/2015] [Accepted: 02/17/2015] [Indexed: 11/29/2022]
Abstract
Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.
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Affiliation(s)
- Jared A Grummer
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA, 98195-1800, USA
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Blair C, Méndez de la Cruz FR, Law C, Murphy RW. Molecular phylogenetics and species delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest. Mol Phylogenet Evol 2015; 84:254-65. [DOI: 10.1016/j.ympev.2015.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
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Chen JJ, Cui BK, Zhou LW, Korhonen K, Dai YC. Phylogeny, divergence time estimation, and biogeography of the genus Heterobasidion (Basidiomycota, Russulales). FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-014-0317-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gottscho AD. Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America. Biol Rev Camb Philos Soc 2014; 91:235-54. [DOI: 10.1111/brv.12167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 10/28/2014] [Accepted: 11/11/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew D. Gottscho
- Department of Biology; San Diego State University; 5500 Campanile Drive San Diego CA 92182 U.S.A
- Department of Biology; University of California; Riverside CA 92521 U.S.A
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Recuero E, Buckley D, García-París M, Arntzen JW, Cogălniceanu D, Martínez-Solano I. Evolutionary history of Ichthyosaura alpestris (Caudata, Salamandridae) inferred from the combined analysis of nuclear and mitochondrial markers. Mol Phylogenet Evol 2014; 81:207-20. [DOI: 10.1016/j.ympev.2014.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 08/12/2014] [Accepted: 09/15/2014] [Indexed: 10/24/2022]
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Schonhuth S, Lozano-Vilano L, Perdices A, Espinosa H, Mayden RL. Phylogeny, genetic diversity and phylogeography of the genusCodoma(Teleostei, Cyprinidae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susana Schonhuth
- Department of Biology; Saint Louis University; 3507 Laclede Avenue St. Louis MO 63103 USA
| | - Lourdes Lozano-Vilano
- Department of Biology; Saint Louis University; 3507 Laclede Avenue St. Louis MO 63103 USA
| | - Anabel Perdices
- Department of Biology; Saint Louis University; 3507 Laclede Avenue St. Louis MO 63103 USA
| | - Héctor Espinosa
- Department of Biology; Saint Louis University; 3507 Laclede Avenue St. Louis MO 63103 USA
| | - Richard L. Mayden
- Department of Biology; Saint Louis University; 3507 Laclede Avenue St. Louis MO 63103 USA
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Moreno-Letelier A, Mastretta-Yanes A, Barraclough TG. Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: clues for the diversification of North American conifers. THE NEW PHYTOLOGIST 2014; 203:335-347. [PMID: 24611638 DOI: 10.1111/nph.12761] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/08/2014] [Indexed: 06/03/2023]
Abstract
Western North America and Mexico contain a large number of conifer species. This diversity could be the product of orographic and climate changes of the late Tertiary and Quaternary. In this study, we focus on the evolutionary history of Juniperus blancoi, in order to determine the impact of climate change and environmental heterogeneity on population differentiation. We estimated the population structure, phylogenetic relationships and historical demography of J. blancoi populations using nuclear genes. We correlated genetic structure with ecological differentiation, divergence times and changes in population size. Populations of J. blancoi are differentiated into three lineages that correspond to low-, mid- and high-altitude populations. The three groups diversified in the late Miocene, early Pliocene, with only a few events of gene flow since then. Two lineages in the north exhibited a pattern of population growth during the Pleistocene that could be linked to climate changes. Populations of J. blancoi experienced significant ecological differentiation and early divergence events, which correspond to periods of global cooling and mountain uplift during the Miocene. This suggests that mountain ranges in tropical and subtropical latitudes play an important role in the speciation and persistence of conifer taxa in diversity hotspots, by providing diverse environmental conditions.
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Torstrom SM, Pangle KL, Swanson BJ. Shedding subspecies: The influence of genetics on reptile subspecies taxonomy. Mol Phylogenet Evol 2014; 76:134-43. [DOI: 10.1016/j.ympev.2014.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/08/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
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Streicher JW, García-Vázquez UO, Ponce-Campos P, Flores-Villela O, Campbell JA, Smith EN. Evolutionary relationships amongst polymorphic direct-developing frogs in theCraugastor rhodopisSpecies Group (Anura: Craugastoridae). SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.882428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Arbeláez-Cortés E, Milá B, Navarro-Sigüenza AG. Multilocus analysis of intraspecific differentiation in three endemic bird species from the northern Neotropical dry forest. Mol Phylogenet Evol 2014; 70:362-77. [DOI: 10.1016/j.ympev.2013.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 10/04/2013] [Accepted: 10/06/2013] [Indexed: 11/16/2022]
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Genetic differentiation and species cohesion in two widespread Central American Begonia species. Heredity (Edinb) 2013; 112:382-90. [PMID: 24220088 DOI: 10.1038/hdy.2013.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/20/2013] [Accepted: 09/19/2013] [Indexed: 11/08/2022] Open
Abstract
Begonia is one of the ten largest plant genera, with over 1500 species. This high species richness may in part be explained by weak species cohesion, which has allowed speciation by divergence in allopatry. In this study, we investigate species cohesion in the widespread Central American Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations at microsatellite loci. We then test for post-zygotic reproductive barriers using experimental crosses, and assess whether sterility barriers are related to intraspecific changes in genome size, indicating major genome restructuring between isolated populations. Strong population substructure was found for B. heracleifolia (FST=0.364, F'ST=0.506) and B. nelumbiifolia (FST=0.277, F'ST=0.439), and Bayesian admixture analysis supports the division of most populations into discrete genetic clusters. Moderate levels of inferred selfing (B. heracleifolia s=0.40, B. nelumbiifolia s=0.62) and dispersal limitation are likely to have contributed to significant genetic differentiation (B. heracleifolia Jost's D=0.274; B. nelumbiifolia D=0.294). Interpopulation crosses involving a divergent B. heracleifolia population with a genome size ∼10% larger than the species mean had a ∼20% reduction in pollen viability compared with other outcrosses, supporting reproductive isolation being polymorphic within the species. The population genetic data suggest that Begonia populations are only weakly connected by gene flow, allowing reproductive barriers to accumulate between the most isolated populations. This supports allopatric divergence in situ being the precursor of speciation in Begonia, and may also be a common speciation mechanism in other tropical herbaceous plant groups.
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Castañeda-Rico S, León-Paniagua L, Vázquez-Domínguez E, Navarro-Sigüenza AG. Evolutionary diversification and speciation in rodents of the Mexican lowlands: the Peromyscus melanophrys species group. Mol Phylogenet Evol 2013; 70:454-63. [PMID: 24140979 DOI: 10.1016/j.ympev.2013.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 10/26/2022]
Abstract
Despite some studies of the species groups within the genus Peromyscus have been performed, both evolutionary relationships among species within groups and group composition have remained controversial. In this study, we address phylogenetic relationships among species in the Peromyscus melanophrys group (P. melanophrys, P. perfulvus, and P. mekisturus), using a molecular phylogenetic analysis. This analysis is the first to include the poorly known P. mekisturus. We conducted maximum likelihood and Bayesian inference analyses with the ND3, tRNA-Arginine, ND4L, and partial ND4 mitochondrial genes, and the GHR nuclear gene. We consistently recovered a P. melanophrys group that is monophyletic with respect to the set of outgroups. Also, we recovered two distinct clades within P. perfulvus and two within P. melanophrys, one of which contain P. mekisturus among other P. melanophrys, all with geographic consistency. According to our divergence time estimates, the P. melanophrys group diverged during the Pliocene and the main diversification events within the group occurred at the end of the Pliocene and through the Pleistocene.
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Affiliation(s)
- Susette Castañeda-Rico
- Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P. 70-399, Ciudad Universitaria, México, DF 04510, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Coyoacán, México, DF 04510, Mexico.
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Monteiro FA, Peretolchina T, Lazoski C, Harris K, Dotson EM, Abad-Franch F, Tamayo E, Pennington PM, Monroy C, Cordon-Rosales C, Salazar-Schettino PM, Gómez-Palacio A, Grijalva MJ, Beard CB, Marcet PL. Phylogeographic pattern and extensive mitochondrial DNA divergence disclose a species complex within the Chagas disease vector Triatoma dimidiata. PLoS One 2013; 8:e70974. [PMID: 23940678 PMCID: PMC3733668 DOI: 10.1371/journal.pone.0070974] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Triatoma dimidiata is among the main vectors of Chagas disease in Latin America. However, and despite important advances, there is no consensus about the taxonomic status of phenotypically divergent T. dimidiata populations, which in most recent papers are regarded as subspecies. METHODOLOGY AND FINDINGS A total of 126 cyt b sequences (621 bp long) were produced for specimens from across the species range. Forty-seven selected specimens representing the main cyt b clades observed (after a preliminary phylogenetic analysis) were also sequenced for an ND4 fragment (554 bp long) and concatenated with their respective cyt b sequences to produce a combined data set totalling 1175 bp/individual. Bayesian and Maximum-Likelihood phylogenetic analyses of both data sets (cyt b, and cyt b+ND4) disclosed four strongly divergent (all pairwise Kimura 2-parameter distances >0.08), monophyletic groups: Group I occurs from Southern Mexico through Central America into Colombia, with Ecuadorian specimens resembling Nicaraguan material; Group II includes samples from Western-Southwestern Mexico; Group III comprises specimens from the Yucatán peninsula; and Group IV consists of sylvatic samples from Belize. The closely-related, yet formally recognized species T. hegneri from the island of Cozumel falls within the divergence range of the T. dimidiata populations studied. CONCLUSIONS We propose that Groups I-IV, as well as T. hegneri, should be regarded as separate species. In the Petén of Guatemala, representatives of Groups I, II, and III occur in sympatry; the absence of haplotypes with intermediate genetic distances, as shown by multimodal mismatch distribution plots, clearly indicates that reproductive barriers actively promote within-group cohesion. Some sylvatic specimens from Belize belong to a different species - likely the basal lineage of the T. dimidiata complex, originated ~8.25 Mya. The evidence presented here strongly supports the proposition that T. dimidiata is a complex of five cryptic species (Groups I-IV plus T. hegneri) that play different roles as vectors of Chagas disease in the region.
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Affiliation(s)
- Fernando A Monteiro
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil.
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Reyes-Velasco J, Meik JM, Smith EN, Castoe TA. Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri). Mol Phylogenet Evol 2013; 69:524-34. [PMID: 23916566 DOI: 10.1016/j.ympev.2013.07.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/18/2013] [Accepted: 07/25/2013] [Indexed: 11/20/2022]
Abstract
The longtailed rattlesnakes of western Mexico represent an enigmatic group of poorly known venomous snake species: Crotalus ericsmithi, C. lannomi, and C. stejnegeri. In the 120 years since their discovery, fewer than twenty individuals have been deposited in natural history collections worldwide. These three species share similar morphological traits, including a particularly long tail that has been interpreted as either an ancestral condition among rattlesnakes or as derived within the longtailed group. An understanding of the phylogenetic distinctiveness and relationships among the longtailed rattlesnakes, and their relationships to other rattlesnake groups, has previously been hampered by a dearth of comparative material and tissues for collection of DNA sequence data. Facilitated by the recent availability of tissue samples from multiple individuals of each species, we estimate the phylogenetic relationships among the longtailed rattlesnakes and their placement among other rattlesnake groups, using DNA sequence data from three mitochondrial and three nuclear gene fragments. We explore phylogenetic signal in our data using Bayesian and maximum likelihood methods, species tree analyses and hypothesis testing. Our results strongly support the monophyly of longtailed rattlesnakes and suggest the three species diverged from each other during the mid to late Pliocene or early Pleistocene (~1.5-5.6 mya). Contrary to prevailing hypotheses, we find no evidence for an early or basal divergence of the longtailed clade within the rattlesnake tree, and instead estimate that it diverged relatively recently (~6.8 mya) from its sister lineage, composed of the diamondback rattlesnakes (C. atrox group) and the prairie rattlesnakes (C. viridis group). With our added sampling of lineages and identification of previously used problematic sequences, we provide a revised hypothesis for relationships among Crotalus species, yet underscore the need for future studies and new data to deliver a well-supported robust estimate of rattlesnake relationships.
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Affiliation(s)
- Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010-0498, United States; Entorno Biotico A.C., Simon Bolivar #145, San Pablo, Colima, Colima 28000, Mexico
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Hardy DK, González-Cózatl FX, Arellano E, Rogers DS. Molecular phylogenetics and phylogeographic structure of Sumichrast’s harvest mouse (Reithrodontomys sumichrasti: Cricetidae) based on mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 2013; 68:282-92. [DOI: 10.1016/j.ympev.2013.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
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Mercado-Salas NF, Suárez-Morales E, Maeda-Martínez AM, Silva-Briano M. A new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopidae, Cyclopinae) from the Chihuahuan desert, northern Mexico. Zookeys 2013:1-18. [PMID: 23794845 PMCID: PMC3677353 DOI: 10.3897/zookeys.287.4358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/26/2013] [Indexed: 11/12/2022] Open
Abstract
A new species of the freshwater cyclopoid copepod genus Metacyclops Kiefer, 1927 is described from a single pond in northern Mexico, within the binational area known as the Chihuahuan Desert. This species belongs to a group of Metacyclops species with a 3443 spine formula of swimming legs. It is morphologically similar to Metacyclops lusitanus Lindberg, 1961 but differs from this and other congeners by having a unique combination of characters, including a caudal rami length/width proportion of 3.5–3.8, a innermost terminal seta slightly longer than the outermost terminal seta, intercoxal sclerites of legs 1-4 naked, a strong apical spine of the second endopodal segment of leg 1 and one row of 6-8 small spinules at the insertion of this spine. The finding of this species represents also the first record of the genus in Mexico and the third in North America, where only two other species, Metacyclops gracilis (Lilljeborg, 1853)and Metacyclops cushae Reid, 1991 have been hitherto reported. This is also the first continental record of a species of Metacyclops from an arid environment in the Americas. This species appears to be endemic to the Chihuahuan Desert, thus emphasizing the high endemicity of this area.
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Affiliation(s)
- Nancy F Mercado-Salas
- El Colegio de la Frontera Sur (ECOSUR) Unidad Chetumal, A. P. 424. Chetumal, Quintana Roo 77014, Mexico
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Garrick RC, Nason JD, Fernández-Manjarrés JF, Dyer RJ. Ecological coassociations influence species' responses to past climatic change: an example from a Sonoran Desert bark beetle. Mol Ecol 2013; 22:3345-61. [DOI: 10.1111/mec.12318] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ryan C. Garrick
- Department of Biology; University of Mississippi; Oxford; MS; 38677; USA
| | - John D. Nason
- Department of Ecology, Evolution and Organismal Biology; Iowa State University; Ames; IA; 50011; USA
| | - Juan F. Fernández-Manjarrés
- Laboratoire d'Ecologie, Systématique et Evolution; UMR CNRS 8079; Bât 360; Université Paris-Sud 11; 91405; Orsay Cedex; France
| | - Rodney J. Dyer
- Department of Biology; Virginia Commonwealth University; Richmond; VA; 23284; USA
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Mercado-Salas N, Álvarez-Silva C. A new AcanthocyclopsKiefer, 1927 (Cyclopoida: Cyclopinae) from an ecological reserve in Mexico City. J NAT HIST 2013. [DOI: 10.1080/00222933.2012.742589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Miguez-Gutiérrez A, Castillo J, Márquez J, Goyenechea I. Biogeografía de la Zona de Transición Mexicana con base en un análisis de árboles reconciliados. REV MEX BIODIVERS 2013. [DOI: 10.7550/rmb.32119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ornelas JF, Sosa V, Soltis DE, Daza JM, González C, Soltis PS, Gutiérrez-Rodríguez C, de los Monteros AE, Castoe TA, Bell C, Ruiz-Sanchez E. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica. PLoS One 2013; 8:e56283. [PMID: 23409165 PMCID: PMC3567015 DOI: 10.1371/journal.pone.0056283] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 01/12/2013] [Indexed: 12/01/2022] Open
Abstract
Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests–among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.
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Affiliation(s)
- Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, AC, Xalapa, Veracruz, Mexico.
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Rovito SM, Parra-Olea G, Vásquez-Almazán CR, Luna-Reyes R, Wake DB. Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders. BMC Evol Biol 2012; 12:255. [PMID: 23273329 PMCID: PMC3556321 DOI: 10.1186/1471-2148-12-255] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/12/2012] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton) using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner. RESULTS Deep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems. CONCLUSIONS Species of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B. nympha, in contrast to the other widespread species in the subgenus, may be due to historical forest contraction and more recent range expansion in the region. Phylogeographic data provide substantial insight into the evolutionary history of these morphologically similar species of salamanders, and contribute to our understanding of factors that have generated the high biodiversity of Mesoamerica.
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Affiliation(s)
- Sean M Rovito
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA, 94720-3160, USA
- Instituto de Biología, Universidad Nacional Autónoma de México, AP 70–153, Circuito Exterior, Ciudad Universitaria, CP 04310, México, D.F., México
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, AP 70–153, Circuito Exterior, Ciudad Universitaria, CP 04310, México, D.F., México
| | - Carlos R Vásquez-Almazán
- Museo de Historia Natural, Escuela de Biología, Universidad de San Carlos, Calle Mariscal Cruz 1-56, Zona 10, Ciudad de Guatemala, Guatemala
| | - Roberto Luna-Reyes
- Coordinación Técnica de Investigación, Secretaría de Medio Ambiente e Historia Natural, Av. de los Hombres Ilustres s/n, Fraccionamiento Francisco I. Madero, Tuxtla Gutiérrez, CP 29000, Chiapas, México
| | - David B Wake
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA, 94720-3160, USA
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Klymus KE, Carl Gerhardt H. AFLP markers resolve intra-specific relationships and infer genetic structure among lineages of the canyon treefrog, Hyla arenicolor. Mol Phylogenet Evol 2012; 65:654-67. [DOI: 10.1016/j.ympev.2012.07.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 07/22/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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Harding LE, Dragoo JW. Out of the tropics: a phylogeographic history of the long-tailed weasel,Mustela frenata. J Mammal 2012. [DOI: 10.1644/11-mamm-a-280.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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