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Pérez-Consuegra SG, Sánchez-Tovar L, Rodríguez-Tapia G, Castañeda-Rico S, Vázquez-Domínguez E. Late Pleistocene Altitudinal Segregation and Demography Define Future Climate Change Distribution of the Peromyscus mexicanus Species Group: Conservation Implications. Animals (Basel) 2023; 13:1753. [PMID: 37889659 PMCID: PMC10251973 DOI: 10.3390/ani13111753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 10/29/2023] Open
Abstract
Mountains harbor a significant number of the World's biodiversity, both on tropical and temperate regions. Notably, one crucial gap in conservation is the consideration of historical and contemporary patterns influencing differential distribution in small mammal mountain species and how climate change will affect their distribution and survival. The mice Peromyscus mexicanus species group is distributed across mountains in Guatemala-Chiapas and Central America, which experienced significant effects of glacial and interglacial cycles. We determined phylogeographic and demographic patterns of lowlands and highlands mountain lineages, revealing that the radiation of modern P. mexicanus lineages occurred during the Pleistocene (ca. 2.6 mya) along Nuclear Central America. In concert with climatic cycles and the distribution of habitats, lowland and highland lineages showed recent population size increase and decrease, respectively. We also estimated the current and future distribution ranges for six lineages, finding marked area size increase for two lineages for which vegetation type and distribution would facilitate migrating towards higher elevations. Contrastingly, three lineages showed range size decrease; their ecological requirements make them highly susceptible to future habitat loss. Our findings are clear evidence of the negative impacts of future climate change, while our ability to manage and conserve these vulnerable ecosystems and mountain species is contingent on our understanding of the implications of climate change on the distribution, ecology, and genetics of wildlife populations.
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Affiliation(s)
- Sergio G. Pérez-Consuegra
- Departamento de Ecología, Escuela de Biología, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
- Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
| | - Laura Sánchez-Tovar
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico; (L.S.-T.); (G.R.-T.)
| | - Gerardo Rodríguez-Tapia
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico; (L.S.-T.); (G.R.-T.)
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC 20008, USA;
- Smithsonian-Mason School of Conservation, Front Royal, VA 22630, USA
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico; (L.S.-T.); (G.R.-T.)
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Rivera-Arroyo RC, Escalante-Pliego P, Aguilar-Torres D, Úbeda-Olivas MF. Phylogeography of the white-crowned parrot (Pionus senilis). BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abstract The white-crowned parrot Pionus senilis (von Spix, 1824) is distributed throughout Middle America, inhabiting the Gulf of Mexico coastal area from Tamaulipas (Mexico) to northern Panama. We used mitochondrial data (COI, ND2 and ND4) from 55 specimens to infer phylogenetic relationships, and analyzed the phylogeographic structure, genetic diversity, divergence periods, and historical demography to explore phylogeographic patterns. We found three divergent lineages: two geographically separated by the Isthmus of Tehuantepec, and the third, in Costa Rica by the Nicaragua Depression. The analysis of molecular variance and statistical analyses were consistent with genetically distinct populations. The Central American lineage diverged 1.33 million years ago, whereas the other two lines branched off 1.19 million years ago. This phylogenetic pattern has been reported in other species of Middle American birds.
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3
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Ardón DA, McMahan CD, Velázquez-Velázquez E, Matamoros WA. Testing spatial and environmental factors to explain body shape variation in the widespread Central American Blackbelt cichlid Vieja maculicauda (Teleostei: Cichlidae). NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Body-shape variability may respond to the interaction between history and environment, particularly in species whose range includes known biogeographical barriers. Central America has traditionally been regarded to have functioned as a complete land-bridge connecting two continents since the Plio-Pleistocene and as an incomplete one since much earlier. This history has helped shape species diversification and distributions. Vieja maculicauda is a widely distributed cichlid, found throughout most of the Atlantic slope of Central America, across three of the four geological blocks that make up this region and whose borders are known dispersal barriers. We asked whether there is an effect of geologic blocks on body shape of V. maculicauda as determined by geometric morphometric assessment of 151 individuals from across its range. We asked how much variance in body shape is explained by environmental variables. We used a CVA and a MANCOVA to determine whether a relationship between body shape and geologic blocks exists. For testing body shape correlation against geographic and environmental variables, we used a Mantel test. Our results suggest that body shape in V. maculicauda can be segregated by geologic blocks, while the correlation results showed no strong correlation between our sets of variables.
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McDonough MM, Ferguson AW, Dowler RC, Gompper ME, Maldonado JE. Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification. Mol Phylogenet Evol 2021; 167:107266. [PMID: 34302947 DOI: 10.1016/j.ympev.2021.107266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/28/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Four species of spotted skunks (Carnivora, Mephitidae, Spilogale) are currently recognized: Spilogale angustifrons, S. gracilis, S. putorius, and S. pygmaea. Understanding species boundaries within this group is critical for effective conservation given that regional populations or subspecies (e.g., S. p. interrupta) have experienced significant population declines. Further, there may be currently unrecognized diversity within this genus as some taxa (e.g., S. angustifrons) and geographic regions (e.g., Central America) never have been assessed using DNA sequence data. We analyzed species limits and diversification patterns in spotted skunks using multilocus nuclear (ultraconserved elements) and mitochondrial (whole mitogenomes and single gene analysis) data sets from broad geographic sampling representing all currently recognized species and subspecies. We found a high degree of genetic divergence among Spilogale that reflects seven distinct species and eight unique mitochondrial lineages. Initial divergence between S. pygmaea and all other Spilogale occurred in the Early Pliocene (∼ 5.0 million years ago). Subsequent diversification of the remaining Spilogale into an "eastern" and a "western" lineage occurred during the Early Pleistocene (∼1.5 million years ago). These two lineages experienced temporally coincident patterns of diversification at ∼0.66 and ∼0.35 million years ago into two and ultimately three distinct evolutionary units, respectively. Diversification was confined almost entirely within the Pleistocene during a timeframe characterized by alternating glacial-interglacial cycles, with the origin of this diversity occurring in northeastern Mexico and the southwestern United States of America. Mitochondrial-nuclear discordance was recovered across three lineages in geographic regions consistent with secondary contact, including a distinct mitochondrial lineage confined to the Sonoran Desert. Our results have direct consequences for conservation of threatened populations, or species, as well as for our understanding of the evolution of delayed implantation in this enigmatic group of small carnivores.
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Affiliation(s)
- Molly M McDonough
- Chicago State University Department of Biological Sciences 9501 S. King Drive, WSC 290 Chicago, IL 60628-1598.
| | - Adam W Ferguson
- Gantz Family Collection Center Field Museum 1400 South Lake Shore Drive Chicago, IL 60605
| | - Robert C Dowler
- Department of Biology Angelo State University ASU Station 10890 San Angelo, TX 76909
| | - Matthew E Gompper
- Department of Fish, Wildlife, and Conservation Ecology New Mexico State University Las Cruces, NM 88003
| | - Jesús E Maldonado
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park PO Box 37012 MRC 5503 Washington, DC 20013
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Martínez-López O, Koch JB, Martínez-Morales MA, Navarrete-Gutiérrez D, Enríquez E, Vandame R. Reduction in the potential distribution of bumble bees (Apidae: Bombus) in Mesoamerica under different climate change scenarios: Conservation implications. GLOBAL CHANGE BIOLOGY 2021; 27:1772-1787. [PMID: 33595918 DOI: 10.1111/gcb.15559] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/16/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Bumble bees are an ecologically and economically important group of pollinating insects worldwide. Global climate change is predicted to affect bumble bee ecology including habitat suitability and geographic distribution. Our study aims to estimate the impact of projected climate change on 18 Mesoamerican bumble bee species. We used ecological niche modeling (ENM) using current and future climate emissions scenarios (representative concentration pathway 4.5, 6.0, and 8.5) and models (CCSM4, HadGEM2-AO, and MIROC-ESM-CHEM). Regardless of the scenario and model applied, our results suggest that all bumble bee species are predicted to undergo a reduction in their potential distribution and habitat suitability due to projected climate change. ENMs based on low emission scenarios predict a distribution loss ranging from 7% to 67% depending on the species for the year 2050. Furthermore, we discovered that the reduction of bumble bee geographic range shape will be more evident at the margins of their distribution. The reduction of suitable habitat is predicted to be accompanied by a 100-500 m upslope change in altitude and 1-581 km shift away from the current geographic centroid of a species' distribution. On average, protected natural areas in Mesoamerica cover ~14% of each species' current potential distribution, and this proportion is predicted to increase to ~23% in the high emission climate change scenarios. Our models predict that climate change will reduce Mesoamerican bumble bee habitat suitability, especially for rare species, by reducing their potential distribution ranges and suitability. The small proportion of current and future potential distribution falling in protected natural areas suggests that such areas will likely have marginal contribution to bumble bee habitat conservation. Our results have the capacity to inform stakeholders in designing effective landscape management for bumble bees, which may include developing restoration plans for montane pine oak forests habitats and native flowering plants.
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Affiliation(s)
- Oscar Martínez-López
- Departamento Agricultura, Sociedad y Ambiente, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
- Unidad para el Conocimiento, Uso y Valoración de la Biodiversidad, Centro de Estudios Conservacionistas-CECON, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Guatemala, Guatemala
| | - Jonathan B Koch
- United States Department of Agriculture - Agricultural Research Service - Pacific West Area - Pollinating Insects - Biology, Management, and Systematics Research Unit, Logan, UT, USA
| | - Miguel A Martínez-Morales
- Departamento Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
| | - Darío Navarrete-Gutiérrez
- Departamento de Observación y Estudio de la Tierra, la Atmósfera y el Océano, Grupo: Ecología, paisaje y sustentabilidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
| | - Eunice Enríquez
- Unidad para el Conocimiento, Uso y Valoración de la Biodiversidad, Centro de Estudios Conservacionistas-CECON, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Guatemala, Guatemala
| | - Rémy Vandame
- Departamento Agricultura, Sociedad y Ambiente, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
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Firneno TJ, O'Neill JR, Portik DM, Emery AH, Townsend JH, Fujita MK. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Mol Ecol 2020; 29:3543-3559. [PMID: 32500624 DOI: 10.1111/mec.15496] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/18/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Justin R O'Neill
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Josiah H Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA.,Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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DNA Barcoding and Demographic History of Peromyscus yucatanicus (Rodentia: Cricetidae) Endemic to the Yucatan Peninsula, Mexico. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09510-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Morrone JJ. Regionalización biogeográfica y evolución biótica de México: encrucijada de la biodiversidad del Nuevo Mundo. REV MEX BIODIVERS 2019. [DOI: 10.22201/ib.20078706e.2019.90.2980] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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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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10
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Nigenda-Morales SF, Gompper ME, Valenzuela-Galván D, Lay AR, Kapheim KM, Hass C, Booth-Binczik SD, Binczik GA, Hirsch BT, McColgin M, Koprowski JL, McFadden K, Wayne RK, Koepfli KP. Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America. Mol Phylogenet Evol 2018; 131:149-163. [PMID: 30468940 DOI: 10.1016/j.ympev.2018.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 11/12/2018] [Accepted: 11/16/2018] [Indexed: 11/30/2022]
Abstract
White-nosed coatis (Nasua narica) are widely distributed throughout North, Central, and South America, but the patterns of temporal and spatial diversification that have contributed to this distribution are unknown. In addition, the biogeographic history of procyonid species in the Americas remains contentious. Using sequences from three mitochondrial loci (Cytochrome b, NAHD5 and 16S rRNA; 2201 bp) and genotypes from 11 microsatellite loci, we analyzed genetic diversity to determine phylogeographic patterns, genetic structure, divergence times, and gene flow among Nasua narica populations throughout the majority of the species' range. We also estimated the ancestral geographic range of N. narica and other procyonid species. We found a high degree of genetic structure and divergence among populations that conform to five evolutionarily significant units. The most southerly distributed population (Panama) branched off much earlier (∼3.8 million years ago) than the northern populations (<1.2 million years ago). Estimated gene flow among populations was low and mostly northwards and westwards. The phylogeographic patterns within N. narica are associated with geographic barriers and habitat shifts likely caused by Pliocene-Pleistocene climate oscillations. Significantly, our findings suggest the dispersal of N. narica was south-to-north beginning in the Pliocene, not in the opposite direction during the Pleistocene as suggested by the fossil record, and that the most recent common ancestor for coati species was most likely distributed in South or Central America six million years ago. Our study implies the possibility that the diversification of Nasua species, and other extant procyonid lineages, may have occurred in South America.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Matthew E Gompper
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - David Valenzuela-Galván
- Departamento de Ecología Evolutiva, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Anna R Lay
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Karen M Kapheim
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | | | | | | | - Ben T Hirsch
- Zoology and Ecology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Maureen McColgin
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - John L Koprowski
- School of Natural Resources and the Environment, The University of Arizona, Tucson, AZ 85721, USA
| | - Katherine McFadden
- College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Robert K Wayne
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C. 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg 199034, Russian Federation.
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11
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Ramírez-Barrera SM, Hernández-Baños BE, Jaramillo-Correa JP, Klicka J. Deep divergence of Red-crowned Ant Tanager ( Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica. PeerJ 2018; 6:e5496. [PMID: 30225165 PMCID: PMC6139011 DOI: 10.7717/peerj.5496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/31/2018] [Indexed: 11/20/2022] Open
Abstract
Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.
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Affiliation(s)
- Sandra M Ramírez-Barrera
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seatle, WA, United States of America
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12
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Almendra AL, González-Cózatl FX, Engstrom MD, Rogers DS. Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini). Mol Phylogenet Evol 2018; 128:12-25. [PMID: 29906608 DOI: 10.1016/j.ympev.2018.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 11/17/2022]
Abstract
Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. Unfortunately, the region continues to experience some of the highest deforestation rates in the world. For mammals, the evolutionary relationships of many endemic taxa are controversial, as it is the case for members of the genus Handleyomys. Estimation of a time-calibrated hypothesis for the evolution of these six genera (Euryoryzomys, Handleyomys, Hylaeamys, Nephelomys, Oecomys and Transandinomys) supported a monophyletic Handleyomys sensu lato. Based on their distinctive morphology and the amount of inter-generic genetic divergence, Handleyomys sensu stricto, H. alfaroi, the H. chapmani, and the H. melanotis species groups warrant recognition as separate genera. In addition, species delimitation documents the existence of cryptic species-level lineages within H. alfaroi and H. rostratus. Cryptic lineages within H. rostratus exhibited significant niche differentiation, but this was not the pattern among species-level clades within H. alfaroi. Similarly, age-range correlations revealed that niche evolution within Handleyomys is not correlated with evolutionary time, instead, ancestral climate tolerance reconstructions show niche disparities at specific diversification events within the chapmani and melanotis species groups, while the climatic niche of the rest of species of Handleyomys tended to be conservative.
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Affiliation(s)
- Ana Laura Almendra
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos C.P. 62209, Mexico.
| | - Francisco X González-Cózatl
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos C.P. 62209, Mexico
| | - Mark D Engstrom
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S 2C6, Canada
| | - Duke S Rogers
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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Cano EB, Schuster JC, Morrone JJ. Phylogenetics of Ogyges Kaup and the biogeography of Nuclear Central America (Coleoptera, Passalidae). Zookeys 2018; 737:81-111. [PMID: 29674874 PMCID: PMC5904369 DOI: 10.3897/zookeys.737.20741] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/18/2018] [Indexed: 11/18/2022] Open
Abstract
A phylogenetic morphological analysis of the genus Ogyges Kaup, distributed in Nuclear Central America, from Chiapas, Mexico, to northwestern Nicaragua was undertaken. Five species of Proculejus Kaup, distributed north of the Isthmus of Tehuantepec in Mexico, were selected as outgroup. Ogyges was recovered as monophyletic with three species groups: championi, laevissimus, and crassulus. Each species group shows a distinct, generally allopatric distribution. The O. championi species group, with ten species, is distributed in the Maya block, more specifically in the mountainous system north of the Motozintla-Comaltitlán fault in Chiapas, and north of the dry valleys of the Cuilco and Motagua rivers in Guatemala. The two remaining species groups are distributed in the Chortis block. The O. laevissimus species group, including seven species, ranges mostly along the Pacific Volcanic Chain from Guatemala to El Salvador, and from southeastern Honduras to the northwestern area of Nicaragua. The O. crassulus species group, with ten species, is distributed from northeastern Guatemala (Merendón) to northern Honduras. The Isthmus of Tehuantepec in Mexico, the Motagua-Cuilco and Motozintla-Comaltitlán sutures zones in Chiapas and Guatemala, the lowland valleys of Colón and Comalí rivers between Nicaragua and Honduras (or, perhaps, the northern suture of the Siuna Terrane in Nicaragua), the Guayape fault system in Honduras, and the intricate dry valleys of Ulúa-Chamelecón-Olancho in Honduras, are hypothesized to have acted as barriers that affected the geographical distribution of Ogyges, as well as probably other montane organisms.
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Affiliation(s)
- Enio B. Cano
- Museo de Zoología "Alfonso L. Herrera", Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apdo. postal 70-399, 04510 Mexico City, Mexico
- Universidad del Valle de Guatemala, Apartado Postal 82, 01901 Guatemala, Guatemala
- Museo de Historia Natural, Escuela de Biología, Universidad de San Carlos de Guatemala, Calle Mariscal Cruz, 1-56, zona 10, Guatemala, Guatemala
| | - Jack C. Schuster
- Universidad del Valle de Guatemala, Apartado Postal 82, 01901 Guatemala, Guatemala
| | - Juan J. Morrone
- Museo de Zoología "Alfonso L. Herrera", Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apdo. postal 70-399, 04510 Mexico City, Mexico
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A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica. Mol Phylogenet Evol 2018; 122:80-94. [PMID: 29407482 DOI: 10.1016/j.ympev.2018.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/27/2018] [Accepted: 01/27/2018] [Indexed: 01/20/2023]
Abstract
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
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15
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Porter CA, Beasley NE, Ordóñez-Garza N, Lindsey LL, Rogers DS, Lewis-Rogers N, Sites JW, Bradley RD. A new species of big-eared climbing rat, genus Ototylomys (Cricetidae: Tylomyinae), from Chiapas, Mexico. J Mammal 2017; 98:1310-1329. [PMID: 29674786 PMCID: PMC5901089 DOI: 10.1093/jmammal/gyx096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 07/20/2017] [Indexed: 11/16/2022] Open
Abstract
An allopatric population of big-eared climbing rats (Ototylomys) from the Northern Highlands of Chiapas, Mexico, is described as a new species. The new taxon is part of a unique montane rainforest community that includes several other endemic species in the limited geographic range between the Río Grijalva and the Central Depression of Chiapas. Several cranial, external, and molecular characters distinguish this new species of big-eared climbing rat from its more widely distributed congener, Ototylomys phyllotis. We performed principal component and discriminate function analyses of cranial measurements, and found that specimens of the new species consistently could be distinguished from other Ototylomys with strong statistical support. Compared with exemplars of Ototylomys from elsewhere in their range, the new species possesses a karyotype that differs by 3 additional biarmed chromosome pairs, is fixed or nearly fixed for distinct electromorphs at 12 allozyme loci, and the mean genetic distance exceeds 14%, based on comparisons of the mitochondrial cytochrome b gene between the new species of Ototylomys and representatives of O. phyllotis. The restricted distribution in montane karst rainforest suggests that the species and its habitat may be a matter of conservation concern. Una población alopátrica de rata orejuda trepadora (Ototylomys) de las Tierras Altas del Norte de Chiapas, México se describe como una nueva especie. El nuevo taxón es parte de una comunidad única de bosque lluvioso montano que incluye varias especies endémicas en el área de distribución geográfica limitada entre el Río Grijalva y la Depresión Central de Chiapas. Varios caracteres craneales, externos, y moleculares distinguen la nueva rata orejuda trepadora de su congénere más ampliamente distribuido, Ototylomys phyllotis. Se realizaron análisis de componentes principales y de función discriminante de los caracteres craneales, y se encontró que los especímenes de La Pera fueron consistentemente distinguidos de otros Ototylomys con un fuerte soporte estadístico. En comparación con ejemplares de Ototylomys del rango, la nueva especie posee un cariotipo que difiere por 3 pares adicionales de cromosomas biarmados, está fijo o casi fijo por distintos electromorfos en 12 loci alozímicos. Adicionalmente, la media de la distancia genética comparada del gen mitochondrial citocromo b entre la nueva especie de Ototylomys y representantes de O. phyllotis, excede el 14%. La distribución restringida en el bosque lluvioso montano kárstico sugiere que la especie y su hábitat pueden ser de importancia para la conservación.
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Affiliation(s)
- Calvin A Porter
- Department of Biology, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, LA 70125, USA (CAP, NEB)
| | - Nia E Beasley
- Department of Biology, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, LA 70125, USA (CAP, NEB)
| | - Nicté Ordóñez-Garza
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX 79409, USA (NO-G, RDB)
| | - Laramie L Lindsey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA (LLL, RDB)
| | - Duke S Rogers
- Department of Biology and Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA (DSR, JWSJr)
| | - Nicole Lewis-Rogers
- Department of Zoology, Weber State University, 2505 University Circle, Ogden, UT 84408, USA (NL-R)
| | - Jack W Sites
- Department of Biology and Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA (DSR, JWSJr)
| | - Robert D Bradley
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX 79409, USA (NO-G, RDB).,Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA (LLL, RDB)
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16
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Pérez-Consuegra SG, Vázquez-Domínguez E. Intricate evolutionary histories in montane species: a phylogenetic window into craniodental discrimination in thePeromyscus mexicanusspecies group (Mammalia: Rodentia: Cricetidae). J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergio G. Pérez-Consuegra
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de México Mexico
- Museo de Historia Natural; Universidad de San Carlos de Guatemala; Ciudad de Guatemala Guatemala
- Posgrado en Ciencias Biológicas; Universidad Nacional Autónoma de México; Coyoacán Ciudad de México Mexico
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ciudad Universitaria; Ciudad de México Mexico
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17
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Population genetics and geometric morphometrics of the Bombus ephippiatus species complex with implications for its use as a commercial pollinator. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0903-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Jiménez RA, Ornelas JF. Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective. PeerJ 2016; 4:e1556. [PMID: 26788433 PMCID: PMC4715438 DOI: 10.7717/peerj.1556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/11/2015] [Indexed: 11/20/2022] Open
Abstract
The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers.
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Affiliation(s)
- Rosa Alicia Jiménez
- Departamento de Biología Evolutiva, Instituto de Ecología A.C. , Xalapa , Veracruz , Mexico
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología A.C. , Xalapa , Veracruz , Mexico
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19
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Ortiz-Ramírez MF, Andersen MJ, Zaldívar-Riverón A, Ornelas JF, Navarro-Sigüenza AG. Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush (Catharus frantzii; Aves: Turdidae). Mol Phylogenet Evol 2015; 94:74-86. [PMID: 26302950 DOI: 10.1016/j.ympev.2015.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 01/29/2023]
Abstract
Montane barriers influence the evolutionary history of lineages by promoting isolation of populations. The effects of these historical processes are evident in patterns of differentiation among extant populations, which are often expressed as genetic and behavioral variation between populations. We investigated the effects of geographic barriers on the evolutionary history of a Mesoamerican bird by studying patterns of genetic and vocal variation in the Ruddy-capped Nightingale-Thrush (Turdidae: Catharus frantzii), a non-migratory oscine bird that inhabits montane forests from central Mexico to Panama. We reconstructed the phylogeographic history and estimated divergence times between populations using Bayesian and maximum likelihood methods. We found strong support for the existence of four mitochondrial lineages of C. frantzii corresponding to isolated mountain ranges: Sierra Madre Oriental; Sierra Madre del Sur; the highlands of Chiapas, Guatemala, and El Salvador; and the Talamanca Cordillera. Vocal features in C. frantzii were highly variable among the four observed clades, but vocal variation and genetic variation were uncorrelated. Song variation in C. frantzii suggests that sexual selection and cultural drift could be important factors driving song differentiation in C. frantzii.
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Affiliation(s)
- Marco F Ortiz-Ramírez
- Museo de Zoología, Facultad de Ciencias, UNAM, Apartado Postal 70-399, México, D. F. 04510, Mexico; Posgrado en Ciencias Biológicas, UNAM, Mexico.
| | - Michael J Andersen
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, UNAM, Apartado Postal 70-233, México, D. F. 04510, Mexico
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20
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Rovito SM, Parra-Olea G, Recuero E, Wake DB. Diversification and biogeographical history of Neotropical plethodontid salamanders. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12271] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean M. Rovito
- Museum of Vertebrate Zoology; University of California; 3101 Valley Life Sciences Building Berkeley CA 94720-3160 USA
- Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153 Circuito Exterior Ciudad Universitaria México DF CP 04510 México
| | - Gabriela Parra-Olea
- Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153 Circuito Exterior Ciudad Universitaria México DF CP 04510 México
| | - Ernesto Recuero
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; AP 70-275 Ciudad Universitaria México DF 04510 Mexico
| | - David B. Wake
- Museum of Vertebrate Zoology; University of California; 3101 Valley Life Sciences Building Berkeley CA 94720-3160 USA
- Department of Integrative Biology; University of California; 3040 Valley Life Sciences Building Berkeley CA 94720-3140 USA
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21
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Pérez Consuegra SG, Vázquez-Domínguez E. Mitochondrial diversification of the Peromyscus mexicanus
species group in Nuclear Central America: biogeographic and taxonomic implications. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sergio Guillermo Pérez Consuegra
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ciudad Universitaria México DF México
- Museo de Historia Natural; Universidad de San Carlos de Guatemala; Ciudad de Guatemala, Guatemala México
- Posgrado en Ciencias Biológicas; Universidad Nacional Autónoma de México; Coyoacán México DF México
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ciudad Universitaria México DF México
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22
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Gutiérrez-García TA, Vázquez-Domínguez E, Arroyo-Cabrales J, Kuch M, Enk J, King C, Poinar HN. Ancient DNA and the tropics: a rodent's tale. Biol Lett 2015; 10:rsbl.2014.0224. [PMID: 24899682 DOI: 10.1098/rsbl.2014.0224] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodent's tale suggests that the sister group to modern O. phyllotis arose during the Miocene-Pliocene, diversified during the Pleistocene and went extinct in the Holocene.
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Affiliation(s)
- Tania A Gutiérrez-García
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria 04510, México
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria 04510, México
| | - Joaquín Arroyo-Cabrales
- Laboratorio de Arqueozoología, Instituto Nacional de Antropología e Historia, Moneda no. 16, Centro 06060, Distrito Federal, México
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
| | - Christine King
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
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23
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Ordóñez-Garza N, Thompson CW, Unkefer MK, Edwards CW, Owen JG, Bradley RD. Systematics of theNeotoma mexicanaspecies group (Mammalia: Rodentia: Cricetidae) in Mesoamerica: new molecular evidence on the status and relationships ofN. ferrugineaTomes, 1862. P BIOL SOC WASH 2014. [DOI: 10.2988/0006-324x-127.3.518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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24
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Guevara L, Sánchez-Cordero V, León-Paniagua L, Woodman N. A new species of small-eared shrew (Mammalia, Eulipotyphla,Cryptotis) from the Lacandona rain forest, Mexico. J Mammal 2014. [DOI: 10.1644/14-mamm-a-018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Malpica A, Ornelas JF. Postglacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad-tailed hummingbird (Selasphorus platycercus). Mol Ecol 2014; 23:435-52. [DOI: 10.1111/mec.12614] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 11/13/2013] [Accepted: 11/15/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Andreia Malpica
- Departamento de Biología Evolutiva; Instituto de Ecología, AC; Carretera antigua a Coatepec No. 351, El Haya Xalapa Veracruz 91070 México
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva; Instituto de Ecología, AC; Carretera antigua a Coatepec No. 351, El Haya Xalapa Veracruz 91070 México
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26
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Rodríguez-Gómez F, Ornelas JF. Genetic divergence of the Mesoamerican azure-crowned hummingbird (Amazilia cyanocephala
, Trochilidae) across the Motagua-Polochic-Jocotán fault system. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Flor Rodríguez-Gómez
- Departamento de Biología Evolutiva; Instituto de Ecología, A.C.; Xalapa Veracruz México
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27
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Razo-Mendivil U, Vázquez-Domínguez E, de León GPP. Discordant genetic diversity and geographic patterns between Crassicutis cichlasomae (Digenea: Apocreadiidae) and its cichlid host, "Cichlasoma" urophthalmus (Osteichthyes: Cichlidae), in Middle-America. J Parasitol 2013; 99:978-88. [PMID: 23859473 DOI: 10.1645/13-225.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genetic analyses of hosts and their parasites are key to understand the evolutionary patterns and processes that have shaped host-parasite associations. We evaluated the genetic structure of the digenean Crassicutis cichlasomae and its most common host, the Mayan cichlid "Cichlasoma" urophthalmus, encompassing most of their geographical range in Middle-America (river basins in southeastern Mexico, Belize, and Guatemala together with the Yucatan Peninsula). Genetic diversity and structure analyses were done based on 167 cytochrome c oxidase subunit 1 sequences (330 bp) for C. cichlasomae from 21 populations and 161 cytochrome b sequences (599 bp) for "C." urophthalmus from 26 populations. Analyses performed included phylogenetic tree estimation under Bayesian inference and maximum likelihood analysis, genetic diversity, distance and structure estimates, haplotype networks, and demographic evaluations. Crassicutis cichlasomae showed high genetic diversity values and genetic structuring, corresponding with 4 groups clearly differentiated and highly divergent. Conversely, "C." urophthalmus showed low levels of genetic diversity and genetic differentiation, defined as 2 groups with low divergence and with no correspondence with geographical distribution. Our results show that species of cichlids parasitized by C. cichlasomae other than "C." urophthalmus, along with multiple colonization events and subsequent isolation in different basins, are likely factors that shaped the genetic structure of the parasite. Meanwhile, historical long-distance dispersal and drought periods during the Holocene, with significant population size reductions and fragmentations, are factors that could have shaped the genetic structure of the Mayan cichlid.
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Affiliation(s)
- Ulises Razo-Mendivil
- Departamento de Ecología de la Biodiversidad. Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria, México DF, 04510, México. Correspondence should be sent to:
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