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Pan T, Zhang C, Orozco Terwengel P, Wang H, Ding L, Yang L, Hu C, Li W, Zhou W, Wu X, Zhang B. Comparative phylogeography reveals dissimilar genetic differentiation patterns in two sympatric amphibian species. Integr Zool 2024; 19:863-886. [PMID: 37880913 DOI: 10.1111/1749-4877.12764] [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] [Indexed: 10/27/2023]
Abstract
Global climate change is expected to have a profound effect on species distribution. Due to the temperature constraints, some narrow niche species could shift their narrow range to higher altitudes or latitudes. In this study, we explored the correlation between species traits, genetic structure, and geographical range size. More specifically, we analyzed how these variables are affected by differences in fundamental niche breadth or dispersal ability in the members of two sympatrically distributed stream-dwelling amphibian species (frog, Quasipaa yei; salamander, Pachyhynobius shangchengensis), in Dabie Mountains, East China. Both species showed relatively high genetic diversity in most geographical populations and similar genetic diversity patterns (JTX, low; BYM, high) correlation with habitat changes and population demography. Multiple clustering analyses were used to disclose differentiation among the geographical populations of these two amphibian species. Q. yei disclosed the relatively shallow genetic differentiation, while P. shangchengensis showed an opposite pattern. Under different historical climatic conditions, all ecological niche modeling disclosed a larger suitable habitat area for Q. yei than for P. shangchengensis; these results indicated a wider environment tolerance or wider niche width of Q. yei than P. shangchengensis. Our findings suggest that the synergistic effects of environmental niche variation and dispersal ability may help shape genetic structure across geographical topology, particularly for species with extremely narrow distribution.
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Affiliation(s)
- Tao Pan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Caiwen Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | | | - Hui Wang
- College of Food and Bioengineering, Bengbu University, Bengbu, China
| | - Ling Ding
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Liuyang Yang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wengang Li
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Wenliang Zhou
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiaobing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
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Hubbs NW, Hurt CR, Niedzwiecki J, Leckie B, Withers D. Conservation genomics of urban populations of Streamside Salamander (Ambystoma barbouri). PLoS One 2022; 17:e0260178. [PMID: 35771804 PMCID: PMC9246143 DOI: 10.1371/journal.pone.0260178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
In Tennessee, populations of the state endangered Streamside Salamander (Ambystoma barbouri) are in decline as their distribution lies mostly within rapidly developing areas in the Nashville Basin. Information regarding the partitioning of genetic variation among populations of A. barbouri and the taxonomic status of these populations relative to northern populations and their congener, the Small-mouthed Salamander (A. texanum), have important implications for management and conservation of this species. Here we combined mitochondrial sequencing and genome-wide single nucleotide polymorphism (SNP) data generated using Genotyping-by-Sequencing (GBS) to investigate patterns of genetic variation within Tennessee populations of A. barbouri, to assess their relationship to populations in Kentucky, and to examine their phylogenetic relationship to the closely related A. texanum. Results from phylogenetic reconstructions reveal a complex history of Tennessee A. barbouri populations with regards to northern populations, unisexual A. barbouri, and A. texanum. Patterns of mitochondrial sequence variation suggest that A. barbouri may have originated within Tennessee and expanded north multiple times into Kentucky, Ohio, Indiana, and West Virginia. Phylogenetic reconstructions based on genome-wide SNP data contradict results based on mitochondrial DNA and correspond to geographic and taxonomic boundaries. Variation in allele frequencies at SNP genotypes, as identified by multivariate analyses and Bayesian assignment tests, identified three evolutionary significant units (ESUs) for A. barbouri within Tennessee. Collectively, these results emphasize the need for prioritizing conservation needs for Tennessee populations of A. barbouri to ensure the long-term persistence of this species.
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Affiliation(s)
- N. Wade Hubbs
- Department of Biology, Tennessee Technological University, Cookeville, TN, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Carla R. Hurt
- Department of Biology, Tennessee Technological University, Cookeville, TN, United States of America
- * E-mail:
| | | | - Brian Leckie
- Department of Biology, Tennessee Technological University, Cookeville, TN, United States of America
| | - David Withers
- Tennessee Department of Environment and Conservation, Nashville, TN, United States of America
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Sunny A, López‐Sánchez M, Ramírez‐Corona F, Suárez‐Atilano M, González‐Fernández A. Genetic diversity and functional connectivity of a critically endangered salamander. Biotropica 2021. [DOI: 10.1111/btp.13025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas Universidad Autónoma del Estado de México Estado de México Mexico
| | - Monserrat López‐Sánchez
- Centro de Investigación en Ciencias Biológicas Aplicadas Universidad Autónoma del Estado de México Estado de México Mexico
| | - Fabiola Ramírez‐Corona
- Taller de Sistemática y Biogeografía Departamento de Biología Evolutiva Facultad de Ciencias Universidad Nacional Autónoma de México Mexico City Mexico
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Geographic patterns of genomic variation in the threatened Salado salamander, Eurycea chisholmensis. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01364-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Shaney KJ, Diaz-Ramirez LG, Espindola S, Castañeda-Rico S, Berovides-Álvarez V, Vázquez-Domínguez E. Defining intraspecific conservation units in the endemic Cuban Rock Iguanas (Cyclura nubila nubila). Sci Rep 2020; 10:21607. [PMID: 33303852 PMCID: PMC7729961 DOI: 10.1038/s41598-020-78664-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
Defining conservation units is an important step in species management and requires interpretation of the genetic diversity and ecological function of the taxon being considered. We used the endemic Cuban Rock Iguanas (Cyclura nubila nubila) as a model to highlight this challenge and examined patterns of its intraspecific genetic diversity across Cuba. We evaluated nuclear (microsatellite loci) and mitochondrial diversity across eight populations from the island and its off-shore cays, and applied the population genetics results for assignment of Management Unit (MU) status and Evolutionary Significant Units (ESUs) based on phylogeographic and time of divergence information. We identified at least six distinct Cuban Rock Iguana MUs, encompassing demographically isolated and genetically differentiated populations across Cuba, most with low effective population size, declining populations, and with high risk of inbreeding and genetic drift. Hence, each MU should be considered of urgent conservation priority. Given the key ecological seed dispersal role of C. n. nubila, the disappearance of any MU could trigger the loss of local ecological functional diversity and major negative impacts on their ecosystems. Two divergent ESUs were also identified, exhibiting an historical east-west geographic separation on Cuba. Based on a Caribbean phylogeographic assessment, our findings strengthen the conclusion that all geographically and evolutionarily differentiated Cyclura species and subspecies across the archipelago warrant ESU distinction.
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Affiliation(s)
- Kyle J Shaney
- Departamento de Ecología de La Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - L Grisell Diaz-Ramirez
- Division of Geriatrics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sayra Espindola
- Departamento de Ecología de La Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Vicente Berovides-Álvarez
- Facultad de Ciencias Biológicas, Universidad de La Habana, Calle 25, # 455, entre J e I, Vedado, Ciudad Habana, Cuba
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de La Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
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Hernández VV, Lemos-Espinal JA, Smith GR, Montoya-Ayala R. NATURAL HISTORY OBSERVATIONS OF AMBYSTOMA ALTAMIRANI AND DRYOPHYTES PLICATUS AT SIERRA DE LAS CRUCES, STATE OF MÉXICO, MEXICO. SOUTHWEST NAT 2020. [DOI: 10.1894/0038-4909-64-2-135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Viridiana Villarreal Hernández
- Laboratorio de Ecología, UBIPRO, Facultad de Estudios Superiores Iztacala-UNAM, Av. Los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Estado de México, Mexico 54090 (VVH, JALE)
| | - Julio A. Lemos-Espinal
- Laboratorio de Ecología, UBIPRO, Facultad de Estudios Superiores Iztacala-UNAM, Av. Los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Estado de México, Mexico 54090 (VVH, JALE)
| | - Geoffrey R. Smith
- Department of Biology, Denison University, Granville, OH 43023 (GRS)
| | - Raymundo Montoya-Ayala
- Laboratorio de Sistemas de Información Geográfica y Análisis Espacial, UBIPRO, Facultad de Estudios Superiores Iztacala-UNAM, Av. Los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Estado de México, Mexico 54090 (RMA)
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Monroy-Vilchis O, Heredia-Bobadilla RL, Zarco-González MM, Ávila-Akerberg V, Sunny A. Genetic diversity and structure of two endangered mole salamander species of the Trans-Mexican Volcanic Belt. HERPETOZOA 2019. [DOI: 10.3897/herpetozoa.32.e38023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The most important factor leading to amphibian population declines and extinctions is habitat degradation and destruction. To help prevent further extinctions, studies are needed to make appropriate conservation decisions in small and fragmented populations. The goal of this study was to provide data from the population genetics of two micro-endemic mole salamanders from the Trans-Mexican Volcanic Belt. Nine microsatellite markers were used to study the population genetics of 152 individuals from twoAmbystomaspecies. We sampled 38 individuals in two localities forA. altamiraniandA. rivualre. We found medium to high levels of genetic diversity expressed as heterozygosity in the populations. However, all the populations presented few alleles per locus and genotypes. We found strong genetic structure between populations for each species. Effective population size was small but similar to that of the studies from other mole salamanders with restricted distributions or with recently fragmented habitats. Despite the medium to high levels of genetic diversity expressed as heterozygosity, we found few alleles, evidence of a genetic bottleneck and that the effective population size is small in all populations. Therefore, this study is important to propose better management plans and conservation efforts for these species.
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Pan T, Zhou K, Zhang S, Shu Y, Zhang J, Li E, Wang M, Yan P, Wu H. Effects of dispersal barriers and geographic distance on the genetic structure of a narrowly distributed frog in a spatially structured landscape. J Zool (1987) 2019. [DOI: 10.1111/jzo.12730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Pan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - K. Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - S.‐L. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - Y.‐L. Shu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - J.‐H. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - E. Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - M.‐S. Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - P. Yan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - H.‐L. Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
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Sunny A, Duarte-deJesus L, Aguilera-Hernández A, Ramírez-Corona F, Suárez-Atilano M, Percino-Daniel R, Manjarrez J, Monroy-Vilchis O, González-Fernández A. Genetic diversity and demography of the critically endangered Roberts' false brook salamander (Pseudoeurycea robertsi) in Central Mexico. Genetica 2019; 147:149-164. [PMID: 30879155 DOI: 10.1007/s10709-019-00058-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/11/2019] [Indexed: 11/28/2022]
Abstract
Land use changes are threatening the maintenance of biodiversity. Genetic diversity is one of the main indicators of biological diversity and is highly important as it shapes the capability of populations to respond to environmental changes. We studied eleven populations of Pseudoeurycea robertsi, a micro-endemic and critically endangered species from the Nevado de Toluca Volcano, a mountain that is part of the Trans-Mexican Volcanic Belt, Mexico. We sequenced the mitochondrial cytochrome b gene from 71 individuals and genotyped 9 microsatellites from 150 individuals. Our results based on the cytochrome b showed two divergent lineages, with moderate levels of genetic diversity and a recently historical demographic expansion. Microsatellite-based results indicated low levels of heterozygosity for all populations and few alleles per locus, as compared with other mole salamander species. We identified two genetically differentiated subpopulations with a significant level of genetic structure. These results provide fundamental data for the development of management plans and conservation efforts for this critically endangered species.
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Affiliation(s)
- Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico.
| | - Luis Duarte-deJesus
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Arlene Aguilera-Hernández
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Fabiola Ramírez-Corona
- Taller de Sistemática y Biogeografía, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Marco Suárez-Atilano
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Ruth Percino-Daniel
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Javier Manjarrez
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Octavio Monroy-Vilchis
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Andrea González-Fernández
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
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Sunny A, Monroy-Vilchis O, Zarco-González MM. Genetic diversity and structure of Crotalus triseriatus, a rattlesnake of central Mexico. J Genet 2018. [DOI: 10.1007/s12041-018-1004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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González-Fernández A, Manjarrez J, García-Vázquez U, D'Addario M, Sunny A. Present and future ecological niche modeling of garter snake species from the Trans-Mexican Volcanic Belt. PeerJ 2018; 6:e4618. [PMID: 29666767 PMCID: PMC5903425 DOI: 10.7717/peerj.4618] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/24/2018] [Indexed: 11/20/2022] Open
Abstract
Land use and climate change are affecting the abundance and distribution of species. The Trans-Mexican Volcanic Belt (TMVB) is a very diverse region due to geological history, geographic position, and climate. It is also one of the most disturbed regions in Mexico. Reptiles are particularly sensitive to environmental changes due to their low dispersal capacity and thermal ecology. In this study, we define the important environmental variables (considering climate, topography, and land use) and potential distribution (present and future) of the five Thamnophis species present in TMVB. To do so, we used the maximum entropy modeling software (MAXENT). First, we modeled to select the most important variables to explain the distribution of each species, then we modeled again using only the most important variables and projected these models to the future considering a middle-moderate climate change scenario (rcp45), and land use and vegetation variables for the year 2050 (generated according to land use changes that occurred between years 2002 and 2011). Arid vegetation had an important negative effect on habitat suitability for all species, and minimum temperature of the coldest month was important for four of the five species. Thamnophis cyrtopsis was the species with the lowest tolerance to minimum temperatures. The maximum temperature of the warmest month was important for T. scalaris and T. cyrtopsis. Low percentages of agriculture were positive for T. eques and T. melanogaster but, at higher values, agriculture had a negative effect on habitat suitability for both species. Elevation was the most important variable to explain T. eques and T. melanogaster potential distribution while distance to Abies forests was the most important variable for T. scalaris and T. scaliger. All species had a high proportion of their potential distribution in the TMVB. However, according to our models, all Thamnophis species will experience reductions in their potential distribution in this region. T. scalaris will suffer the biggest reduction because this species is limited by high temperatures and will not be able to shift its distribution upward, as it is already present in the highest elevations of the TMVB.
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Affiliation(s)
| | - Javier Manjarrez
- Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Uri García-Vázquez
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maristella D'Addario
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
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Heredia-Bobadilla RL, Monroy-Vilchis O, Zarco-González MM, Martínez-Gómez D, Mendoza-Martínez GD, Sunny A. Genetic variability and structure of an isolated population of Ambystoma altamirani, a mole salamander that lives in the mountains of one of the largest urban areas in the world. J Genet 2018; 96:873-883. [PMID: 29321345 DOI: 10.1007/s12041-017-0823-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amphibians are globally threatened by habitat loss and fragmentation; species within the order Ambystoma are not the exception, as there are 18 species of mole salamanders in México, of which 16 are endemic and all species are under some national or international status of protection. The mole salamander, Ambystoma altamirani is a microendemic species, which is distributed in central México, within the trans-Mexican volcanic belt, and is one of the most threatened species due to habitat destruction and the introduction of exotic species. Nine microsatellite markers were used to determine the genetic structure, genetic variability, effective population size, presence of bottlenecks and inbreeding coefficient of one population of A. altamirani to generate information which might help to protect and conserve this threatened species. We found two genetic subpopulations with significant level of genetic structure (FST = 0.005) and high levels of genetic variability (Ho = 0.883; He = 0.621); we also found a small population size (Ne = 8.8), the presence of historical (M = 0.486) and recent bottlenecks under IAM and TPM models, with a low, but significant coefficient of inbreeding (FIS = -0.451). This information will help us to raise conservation strategies of this microendemic mole salamander species.
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Affiliation(s)
- Rosa-Laura Heredia-Bobadilla
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000 Toluca, Estado de México, México.
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No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi). Heredity (Edinb) 2017; 118:424-435. [PMID: 28074844 DOI: 10.1038/hdy.2016.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022] Open
Abstract
Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km2) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies.
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Heredia-Bobadilla RL, Monroy-Vilchis O, Zarco-González MM, Martínez-Gómez D, Mendoza-Martínez GD, Sunny A. Genetic structure and diversity in an isolated population of an endemic mole salamander (Ambystoma rivulare Taylor, 1940) of central Mexico. Genetica 2016; 144:689-698. [PMID: 27796527 DOI: 10.1007/s10709-016-9935-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/18/2016] [Indexed: 11/28/2022]
Abstract
Human activities are affecting the distribution of species worldwide by causing fragmentation and isolation of populations. Isolation and fragmentation lead to populations with lower genetic variability and an increased chance of inbreeding and genetic drift, which results in a loss of biological fitness over time. Studies of the genetic structure of small and isolated populations are critically important for management and conservation decisions. Ambystoma rivulare is a micro-endemic Mexican mole salamander from central Mexico. It is found in the most ecologically disturbed region in Mexico, the Trans-Mexican Volcanic Belt. The goal of this study of the population genetics of the micro-endemic mole salamander was to provide information to be used as a basis for future research and conservation planning of this species and other species of the Ambystoma genus in Mexico. The structural analysis found two subpopulations, one for each river sampled, with no signs of admixture and very high levels of genetic differentiation. Medium to high levels of heterozygosity and few alleles and genotypes were observed. Evidence of an ancestral genetic bottleneck, low values of effective population size, small inbreeding coefficients, and low gene flow were also found.
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Affiliation(s)
- Rosa-Laura Heredia-Bobadilla
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico
| | - Octavio Monroy-Vilchis
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico.
| | - Martha M Zarco-González
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico
| | - Daniel Martínez-Gómez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana Xochimilco, Calz. Del Hueso 1100, Col. Villa Quietud, 04960, Mexico city, Mexico
| | - Germán David Mendoza-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana Xochimilco, Calz. Del Hueso 1100, Col. Villa Quietud, 04960, Mexico city, Mexico
| | - Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico
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15
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Sunny A, Monroy-Vilchis O, Zarco-González MM, Mendoza-Martínez GD, Martínez-Gómez D. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation. Genetica 2015; 143:705-16. [PMID: 26497875 DOI: 10.1007/s10709-015-9868-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/14/2015] [Indexed: 11/30/2022]
Abstract
It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.
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Affiliation(s)
- Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico
| | - Octavio Monroy-Vilchis
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico.
| | - Martha M Zarco-González
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000, Toluca, Estado de México, Mexico
| | - Germán David Mendoza-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana Xochimilco, Calz. Del Hueso 1100, 04960, Col. Villa Quietud, Mexico
| | - Daniel Martínez-Gómez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana Xochimilco, Calz. Del Hueso 1100, 04960, Col. Villa Quietud, Mexico
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16
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Zhang W, Luo Z, Zhao M, Wu H. High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense. Integr Zool 2015; 10:465-81. [PMID: 26037662 DOI: 10.1111/1749-4877.12142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.
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Affiliation(s)
- Wei Zhang
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhenhua Luo
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Mian Zhao
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Hua Wu
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, China
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17
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Sunny A, Monroy-Vilchis O, Reyna-Valencia C, Zarco-González MM. Microhabitat types promote the genetic structure of a micro-endemic and critically endangered mole salamander (Ambystoma leorae) of Central Mexico. PLoS One 2014; 9:e103595. [PMID: 25076052 PMCID: PMC4116214 DOI: 10.1371/journal.pone.0103595] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/01/2014] [Indexed: 11/18/2022] Open
Abstract
The reduced immigration and emigration rates resulting from the lack of landscape connectivity of patches and the hospitality of the intervening matrix could favor the loss of alleles through genetic drift and an increased chance of inbreeding. In order for isolated populations to maintain sufficient levels of genetic diversity and adapt to environmental changes, one important conservation goal must be to preserve or reestablish connectivity among patches in a fragmented landscape. We studied the last known population of Ambystoma leorae, an endemic and critically threatened species. The aims of this study were: (1) to assess the demographic parameters of A. leorae and to distinguish and characterize the microhabitats in the river, (2) to determine the number of existing genetic groups or demes of A. leorae and to describe possible relationships between microhabitats types and demes, (3) to determine gene flow between demes, and (4) to search for geographic locations of genetic discontinuities that limit gene flow between demes. We found three types of microhabitats and three genetically differentiated subpopulations with a significant level of genetic structure. In addition, we found slight genetic barriers. Our results suggest that mole salamander's species are very sensitive to microhabitat features and relatively narrow obstacles in their path. The estimates of bidirectional gene flow are consistent with the pattern of a stepping stone model between demes, where migration occurs between adjacent demes, but there is low gene flow between distant demes. We can also conclude that there is a positive correlation between microhabitats and genetic structure in this population.
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Affiliation(s)
- Armando Sunny
- Estación Biológica Sierra Nanchititla, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Octavio Monroy-Vilchis
- Estación Biológica Sierra Nanchititla, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Carlos Reyna-Valencia
- Estación Biológica Sierra Nanchititla, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Martha M. Zarco-González
- Estación Biológica Sierra Nanchititla, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
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Espindola S, Cuarón AD, Gaggiotti OE, Vázquez-Domínguez E. High genetic structure of the Cozumel Harvest mice, a critically endangered island endemic: conservation implications. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0625-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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