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Kameya M, Watanabe T, Nambu H, Yamazaki Y. Phylogeographic History of Endangered Hokuriku Salamander, Hynobius takedai (Amphibia: Caudata). Zoolog Sci 2024; 41:177-184. [PMID: 38587912 DOI: 10.2108/zs230101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/25/2023] [Indexed: 04/10/2024]
Abstract
Knowledge of the phylogeographic history of organisms is valuable for understanding their evolutionary processes. To the best of our knowledge, the phylogeographic structure of Hokuriku salamander, Hynobius takedai, an endangered species, remains unclear. This study aimed to elucidate the phylogeographic history of H. takedai, which is expected to be strongly influenced by paleogeographic events. Phylogenetic analysis based on partial sequences of the mitochondrial DNA cytochrome b gene confirmed the genetic independence of H. takedai, and the divergence time with closely related species was estimated to be from the Late Pliocene to the Early Pleistocene. In the phylogenetic tree, two clades were identified within H. takedai, and their haplotypes were found in samples collected from the west and east of the distribution range. These intraspecific divergences were strongly influenced by geohistorical subdivisions of the current major distribution areas in the Middle Pleistocene. One clade was further subdivided and its formation may have been influenced by sea level changes in the Late Pleistocene.
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Affiliation(s)
- Mitsushi Kameya
- Faculty of Science, University of Toyama, Toyama 930-8555, Japan
| | - Takumi Watanabe
- Faculty of Science, University of Toyama, Toyama 930-8555, Japan
| | - Hisao Nambu
- Faculty of Science, University of Toyama, Toyama 930-8555, Japan
| | - Yuji Yamazaki
- Faculty of Science, University of Toyama, Toyama 930-8555, Japan,
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Pyron RA, Kakkera A, Beamer DA, O'Connell KA. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype. Mol Ecol 2024; 33:e17219. [PMID: 38015012 DOI: 10.1111/mec.17219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Anvith Kakkera
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University, Greenville, North Carolina, USA
| | - Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
- Deloitte Consulting LLP, Health and Data AI, Arlington, Virginia, USA
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Sunny A, Manjarrez J, Caballero-Viñas C, Bolom-Huet R, Gómez-Ortiz Y, Domínguez-Vega H, Heredia-Bobadilla RL, Torres-Romero EJ, González-Fernández A. Modelling the effects of climate and land-cover changes on the potential distribution and landscape connectivity of three earth snakes (Genus Conopsis, Günther 1858) in central Mexico. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2023; 110:52. [PMID: 37889338 DOI: 10.1007/s00114-023-01880-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
Anthropogenic land use and climate change are the greatest threats to biodiversity, especially for many globally endangered reptile species. Earth snakes (Conopsis spp.) are a poorly studied group endemic to Mexico. They have limited dispersal abilities and specialized niches, making them particularly vulnerable to anthropogenic threats. Species distribution models (SDMs) were used to assess how future climate and land-cover change scenarios might influence the distribution and habitat connectivity of three earth snakes: Conopsis biserialis (Taylor and Smith), C. lineata (Kennicott), and C. nasus (Günther). Two climate models, CNRM-CM5 (CN) and MPI-ESM-LR (MP) (Representative Concentration Pathway 85), were explored with ENMeval Maxent modelling. Important SDM environmental variables and environmental niche overlap between species were also examined. We found that C. biserialis and C. lineata were restricted by maximum temperatures whereas C. nasus was restricted by minimum ones and was more tolerant to arid vegetation. C. biserialis and C. lineata were primarily distributed in the valleys and mountains of the highlands of the TMBV, while C. nasus was mainly distributed in the Altiplano Sur (Zacatecano-Potosino). C. lineata had the smallest potential distribution and suffered the greatest contraction in the future whereas C. nasus was the least affected species in future scenarios. The Sierra de las Cruces and the Sierra Chichinautzin were identified as very important areas for connectivity. Our results suggest that C. lineata may be the most vulnerable of the three species to anthropogenic and climate changes whereas C. nasus seems to be less affected by global warming than the other 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, Estado de México, Mexico.
| | - Javier Manjarrez
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario 100, Colonia Centro, 50000, Toluca, Estado de México, Mexico
| | - Carmen Caballero-Viñas
- Instituto de Geología, Departamento de Paleontología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - René Bolom-Huet
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario 100, Colonia Centro, 50000, Toluca, Estado de México, Mexico
| | - Yuriana Gómez-Ortiz
- División de Desarrollo Sustentable, Universidad Intercultural del Estado de México, Libramiento Francisco Villa SN, 50640, San Felipe del Progreso, Estado de México, Mexico
| | - Hublester Domínguez-Vega
- División de Desarrollo Sustentable, Universidad Intercultural del Estado de México, Libramiento Francisco Villa SN, 50640, San Felipe del Progreso, Estado de México, Mexico
| | - Rosa Laura Heredia-Bobadilla
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario 100, Colonia Centro, 50000, Toluca, Estado de México, Mexico
| | - Erik Joaquín Torres-Romero
- Ingeniería en Biotecnología, Universidad Politécnica de Puebla, San Mateo Cuanalá, Juan C. Bonilla, 72640, Puebla, Mexico
| | - Andrea González-Fernández
- Laboratorio de Análisis Geo-Espacial (LAGE), Instituto de Geografía, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior S/N, Coyoacán, Cd. Universitaria, 04510, Mexico City, Mexico
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Mata-Guel EO, Soh MCK, Butler CW, Morris RJ, Razgour O, Peh KSH. Impacts of anthropogenic climate change on tropical montane forests: an appraisal of the evidence. Biol Rev Camb Philos Soc 2023; 98:1200-1224. [PMID: 36990691 DOI: 10.1111/brv.12950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023]
Abstract
In spite of their small global area and restricted distributions, tropical montane forests (TMFs) are biodiversity hotspots and important ecosystem services providers, but are also highly vulnerable to climate change. To protect and preserve these ecosystems better, it is crucial to inform the design and implementation of conservation policies with the best available scientific evidence, and to identify knowledge gaps and future research needs. We conducted a systematic review and an appraisal of evidence quality to assess the impacts of climate change on TMFs. We identified several skews and shortcomings. Experimental study designs with controls and long-term (≥10 years) data sets provide the most reliable evidence, but were rare and gave an incomplete understanding of climate change impacts on TMFs. Most studies were based on predictive modelling approaches, short-term (<10 years) and cross-sectional study designs. Although these methods provide moderate to circumstantial evidence, they can advance our understanding on climate change effects. Current evidence suggests that increasing temperatures and rising cloud levels have caused distributional shifts (mainly upslope) of montane biota, leading to alterations in biodiversity and ecological functions. Neotropical TMFs were the best studied, thus the knowledge derived there can serve as a proxy for climate change responses in under-studied regions elsewhere. Most studies focused on vascular plants, birds, amphibians and insects, with other taxonomic groups poorly represented. Most ecological studies were conducted at species or community levels, with a marked paucity of genetic studies, limiting understanding of the adaptive capacity of TMF biota. We thus highlight the long-term need to widen the methodological, thematic and geographical scope of studies on TMFs under climate change to address these uncertainties. In the short term, however, in-depth research in well-studied regions and advances in computer modelling approaches offer the most reliable sources of information for expeditious conservation action for these threatened forests.
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Affiliation(s)
- Erik O Mata-Guel
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Malcolm C K Soh
- National Park Boards, 1 Cluny Road, Singapore, 259569, Singapore
| | - Connor W Butler
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Rebecca J Morris
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Orly Razgour
- Biosciences, University of Exeter, Exeter, EX4 4PS, UK
| | - Kelvin S-H Peh
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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Bolom-Huet R, Pacheco XP, Muñoz-Alonso A, Sunny A. Potential Distribution and Connectivity for Two Plethodontid Salamanders: Conservation Areas and Landscape Corridors for Two Endemic Species of México and Guatemala. ENVIRONMENTAL MANAGEMENT 2022; 70:965-977. [PMID: 36038650 DOI: 10.1007/s00267-022-01700-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Habitat loss is one of the most important threats to biodiversity; it alters the habitat connectivity of species and is among the main causes of the global amphibian extinction crisis. Identifying the potential areas of distribution and connectivity of species is of the utmost importance so that informed decisions can be made for the conservation of vulnerable amphibian populations. In this study, we performed species distribution models and used circuit theory to model omnidirectional connectivity for two plethodontid salamanders of conservation concern distributed in the forests of Chiapas, Mexico, and Guatemala (Bolitoglossa franklini and Bolitoglossa lincolni). Potential distribution maps show an affinity for well-preserved montane forests for both species. Likewise, we found that the niches of the species are not similar. The connectivity models show that the main areas of connectivity are in the Meseta Central de Chiapas, Sierra Madre de Chiapas, and the Cordillera Volcánica Guatemalense, in this last range, important areas of connectivity were located, as well as least-cost paths and barriers to the movement of both species. We identified that important areas of climatic suitability and connectivity are not within the protected natural areas and may be threatened by the increasing influence of anthropogenic activities. The results of our study show the importance of preserving the regional forests to ensure the persistence of species with arboreal habits and high sensitivity to habitat transformation, as well as to recognize and prioritize potential areas for management and protection in both southern Mexico and Guatemala.
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Affiliation(s)
- René Bolom-Huet
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario 100, Colonia Centro, 50000, Toluca, Estado de México, Mexico.
| | - Xareni P Pacheco
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario 100, Colonia Centro, 50000, Toluca, Estado de México, Mexico
| | - Antonio Muñoz-Alonso
- El Colegio de la Frontera Sur, Periférico Sur s/n, María Auxiliadora, 29290, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario 100, Colonia Centro, 50000, Toluca, Estado de México, Mexico
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French CM, Berezin CT, Overcast I, Méndez De La Cruz FR, Basu S, Martínez Bernal RL, Murphy RW, Hickerson MJ, Blair C. Forest cover and geographical distance influence fine-scale genetic structure of leaf-toed geckos in the tropical dry forests of western Mexico. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographical distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the Last Glacial Maximum. Landscape genetic analyses suggest that the combination of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) has influenced the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to affect native fauna.
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Affiliation(s)
- Connor M French
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
| | - Casey-Tyler Berezin
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Isaac Overcast
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Institut de Biologie de l’Ecole Normale Superieure , 46 Rue d’Ulm, 75005 Paris , France
- Division of Vertebrate Zoology, American Museum of Natural History , 200 Central Park West, New York, NY 10024 , USA
| | | | - Saptarsi Basu
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
| | | | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum , 100 Queen’s Park, Toronto, ON M5S 2C6 , Canada
| | - Michael J Hickerson
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biology, City College of New York , 160 Convent Avenue, New York, NY 10031 , USA
| | - Christopher Blair
- Biology PhD Program, CUNY Graduate Center , 365 5th Avenue, New York, NY 10016 , USA
- Department of Biological Sciences, New York City College of Technology, The City University of New York , 285 Jay Street, Brooklyn, NY 11201 , USA
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Yousefkhani SSH, Yasser A, Naser M, Yousefabadi F, Gasimova G. Response to Global Warming of Eichwald's Toad, Bufo eichwaldi Litvinchuk, Borkin, Skorinov and Rosanov, 2008 (Anura; Amphibia) in Iran and Azerbaijan. Folia Biol (Praha) 2022. [DOI: 10.3409/fb_70-3.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Global warming is considered to be a major threat to biodiversity and to have an erosive effect on the survival of endangered species. Amphibians are known as a vulnerable group of vertebrates that live and reproduce in both terrestrial and aquatic habitats. The subtropical regions
of the world are among the land areas where amphibians will suffer the most from climate change. In the present study, the effect of climate change on Bufo eichwaldi inhabiting Hyrcanian forests was investigated. According to our results, the lowest temperature in the coldest season
is the most important variable for the presence of this species. Due to the beginning of reproductive activity and mating taking place in late January until the end of February, this variable will have a direct effect on the rate of breeding and thus on the conservation of this species, because
the species can find a new suitable area outside of high humanisation and increase its chance of successful breeding. Of course, climate change will cause the average annual temperature to rise by 2070, and this will favour the early onset of reproduction. Therefore, according to the analysis
and scenarios considered in this study, global warming cannot have a negative effect on the toad species. However, a careful assessment of the status of other competing species in conjunction with the Talysh toad could provide a better explanation of the impact of climate change.
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Affiliation(s)
| | - Amaal Yasser
- Marine Science Centre, University of Basrah, Basrah, Iraq
| | - Murtada Naser
- Marine Science Centre, University of Basrah, Basrah, Iraq
| | - Fariba Yousefabadi
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad (FUM), Iran
| | - Gulbaniz Gasimova
- Department of Terrestrial Vertebrates, Institute of Zoology, Azerbaijan National Academy of Sciences, Baku, Azerbaijan; Life Sciences Department, Khazar University, Baku, Azerbaijan
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Muñoz-Mora VH, Suárez-Atilano M, Maltagliati F, Ramírez-Corona F, Carbajal-Saucedo A, Percino-Daniel R, Langeneck J, D’Addario M, Sunny A. A tale about vipers’ tails: phylogeography of black-tailed rattlesnakes. HERPETOZOA 2022. [DOI: 10.3897/herpetozoa.35.e84297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The phylogenetic relationships among black-tailed rattlesnakes remain poorly understood and some authors indicated that the diversity of this group has been underestimated and additional analyses are required to clarify the biogeographic patterns throughout its distribution in Mexico. Therefore, the aim of this study was to elucidate the phylogenetic relationships among black-tailed rattlesnakes across their range, identifying relative divergence times among the main clades and reconstructing the biogeographical history of the group. Three partial mitochondrial genes (ND4, cytb and ATPase6) and one nuclear gene (RAG1) were sequenced to infer the phylogenetic relationships, through the maximum likelihood and Bayesian inference-based methods; demographic history reconstruction was investigated through Bayesian Skyline plot analysis and the ancestral area reconstruction was carried out considering a Bayesian framework. We found strong evidence that the black-tailed rattlesnakes’ group is composed of six clades, which is in agreement with subspecies previously reported. Divergence time estimation indicated that the origin of the C. molossus group could be traced to the middle of the Miocene (~7.71 Mya). Ancestral area reconstruction indicated that early divergence events occurred in Central Mexico, probably related to the geological dynamics of the Trans-Mexican Volcanic Belt. The lineage C. m. oaxacus is the basal member of the C. molossus group. Furthermore, the combination of geological events and changes in Quaternary vegetation may have contributed to the divergence of C. molossus clades. Our results suggest several clades within C. molossus complex could be potentially recognized as separate species.
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Understanding the drivers of dispersal evolution in range expansions and their ecological consequences. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10166-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractResearch has conclusively demonstrated the potential for dispersal evolution in range expansions and shifts, however the degree of dispersal evolution observed has varied substantially among organisms. Further, it is unknown how the factors influencing dispersal evolution might impact other ecological processes at play. We use an individual-based model to investigate the effects of the underlying genetics of dispersal and mode of reproduction in range expansions and shifts. Consistent with predictions from stationary populations, dispersal evolution increases with sexual reproduction and loci number. Contrary to our predictions, however, increased dispersal does not always improve a population’s ability to track changing conditions. The mate finding Allee effect inherent to sexual reproduction increases extinction risk during range shifts, counteracting the beneficial effect of increased dispersal evolution. Our results demonstrate the importance of considering both ecological and evolutionary processes for understanding range expansions and shifts.
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Vargas-Jaimes J, González-Fernández A, Joaquín Torres-Romero E, Bolom-Huet R, Manjarrez J, Gopar-Merino F, P. Pacheco X, Garrido-Garduño T, Chávez C, Sunny A. Impact of climate and land cover changes on the potential distribution of four endemic salamanders in Mexico. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Teixeira H, Salmona J, Arredondo A, Mourato B, Manzi S, Rakotondravony R, Mazet O, Chikhi L, Metzger J, Radespiel U. Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar. BMC Ecol Evol 2021; 21:197. [PMID: 34727890 PMCID: PMC8561976 DOI: 10.1186/s12862-021-01929-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets. RESULTS We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus. CONCLUSION Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.
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Affiliation(s)
- Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Armando Arredondo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Beatriz Mourato
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Sophie Manzi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
| | - Olivier Mazet
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Lounès Chikhi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559, Hannover, Germany
- Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
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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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13
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Vaissi S, Sharifi M. The least‐cost path analysis of landscape genetics identifies two dispersal routes for the threatened Kaiser's mountain newt (Caudata: Salamandridae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Somaye Vaissi
- Department of Biology, Faculty of Science Razi University Kermanshah Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science Razi University Kermanshah Iran
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14
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Amiri N, Vaissi S, Aghamir F, Saberi‐Pirooz R, Rödder D, Ebrahimi E, Ahmadzadeh F. Tracking climate change in the spatial distribution pattern and the phylogeographic structure of Hyrcanian wood frog,
Rana pseudodalmatina
(Anura: Ranidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Negar Amiri
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Somaye Vaissi
- Department of Biology Faculty of Science Razi University Kermanshah Iran
| | - Fateme Aghamir
- Department of Agroecology Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Reihaneh Saberi‐Pirooz
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Dennis Rödder
- Herpetology Section Zoologisches Forschungsmuseum Alexander Koenig (ZFMK) Bonn Germany
| | - Elham Ebrahimi
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
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15
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Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies. Heredity (Edinb) 2021; 126:776-789. [PMID: 33536637 PMCID: PMC8102559 DOI: 10.1038/s41437-021-00405-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted, leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in the adjacent Montes de Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.
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16
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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17
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Alvarado-Avilés JC, Venegas-Barrera CS, Alvarado-Díaz J, Hernández-Gallegos O, Lourdes Ruiz-Gomez MD, Sánchez-Sánchez H. Potential Distribution of
Plestiodon copei (Squamata: Scincidae), an Endemic and Threatened Lizard of Mexico. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2020. [DOI: 10.2994/10.2994/sajh-d-18-00044.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- J. Carlos Alvarado-Avilés
- Facultad de Ciencias, Universidad Autónoma del Estado de Mexico, El Cerrillo, Toluca, Estado de Mexico, CP 50200, Mexico
| | - Crystian S. Venegas-Barrera
- División de Estudios de Posgrado e Investigación, Instituto Tecnológico de Ciudad Victoria, Blvd. Emilio Portes Gil 1301, Ciudad Victoria, Tamaulipas, CP 87010, Mexico
| | - Javier Alvarado-Díaz
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo. Av. San Juanito Itzicuaro s/n Col. Nva. Esperanza, Morelia, Michoacán. CP 58330, Mexico
| | - Oswaldo Hernández-Gallegos
- Facultad de Ciencias, Universidad Autónoma del Estado de Mexico, El Cerrillo, Toluca, Estado de Mexico, CP 50200, Mexico
| | - Maria de Lourdes Ruiz-Gomez
- Facultad de Ciencias, Universidad Autónoma del Estado de Mexico, El Cerrillo, Toluca, Estado de Mexico, CP 50200, Mexico
| | - Hermilo Sánchez-Sánchez
- Facultad de Ciencias, Universidad Autónoma del Estado de Mexico, El Cerrillo, Toluca, Estado de Mexico, CP 50200, Mexico
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18
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Riparian areas potentially provide crucial corridors through fragmented landscape for black-capped vireo (Vireo atricapilla) source-sink system. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01314-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Lourenço A, Gonçalves J, Carvalho F, Wang IJ, Velo‐Antón G. Comparative landscape genetics reveals the evolution of viviparity reduces genetic connectivity in fire salamanders. Mol Ecol 2019; 28:4573-4591. [DOI: 10.1111/mec.15249] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/22/2019] [Accepted: 09/16/2019] [Indexed: 01/07/2023]
Affiliation(s)
- André Lourenço
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
| | - João Gonçalves
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
| | - Filipe Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
- Department of Zoology and Entomology School of Biological and Environmental Sciences University of Fort Hare Alice South Africa
| | - Ian J. Wang
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - Guillermo Velo‐Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
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20
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Torres-Morales L, Guillén A, Ruiz-Sanchez E. Distinct Patterns of Genetic Connectivity Found for Two Frugivorous Bat Species in Mesoamerica. ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2019.21.1.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Laura Torres-Morales
- División de Posgrado, Instituto de Ecología, A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91070, Mexico
| | - Antonio Guillén
- Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91070, Mexico
| | - Eduardo Ruiz-Sanchez
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Nextipac, Zapopán, Jalisco 45200, Mexico
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21
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Winiarski KJ, Peterman WE, Whiteley AR, McGarigal K. Multiscale resistant kernel surfaces derived from inferred gene flow: An application with vernal pool breeding salamanders. Mol Ecol Resour 2019; 20:97-113. [DOI: 10.1111/1755-0998.13089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Kristopher J. Winiarski
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
- Northeast Climate Adaptation Science Center University of Massachusetts Amherst MA USA
| | - William E. Peterman
- School of Environment and Natural Resources Ohio State University Columbus OH USA
| | - Andrew R. Whiteley
- W.A. Franke College of Forestry and Conservation Wildlife Biology Program University of Montana Missoula MT USA
| | - Kevin McGarigal
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
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22
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Ashrafzadeh MR, Naghipour AA, Haidarian M, Kusza S, Pilliod DS. Effects of climate change on habitat and connectivity for populations of a vulnerable, endemic salamander in Iran. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00637] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Sunny A, Gandarilla-Aizpuro FJ, Monroy-Vilchis O, Zarco-Gonzalez MM. Potential distribution and habitat connectivity of Crotalus triseriatus in Central Mexico. HERPETOZOA 2019. [DOI: 10.3897/herpetozoa.32.e36361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dusky rattlesnake, Crotalustriseriatus, used to be very abundant in many parts of the highlands of central Mexico, but with the increasing human population and associated activities, the rattlesnake habitats and populations have suffered drastic reductions and fragmentation. At the moment, the most important habitat features, associated with the presence of C.triseriatus, the current potential distribution and the landscape connectivity amongst the populations of the State of Mexico and Mexico City, are unknown. Therefore, we used the maximum entropy modelling software (MAXENT) to analyse the current potential distribution and most important habitat features, associated with the presence of the species. The variables with the highest contribution to the model were: proportion of Abies forest, minimum temperature of coldest month, maximum temperature of the warmest month, proportion of Pinus forest and annual precipitation. Furthermore, we found connectivity corridors only within mountain chains. Our results highlight the necessity for conserving the patches of Abies forest and preserving the populations of C.triseriatus and the connectivity of the landscape.
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24
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Tarroso P, Carvalho SB, Velo‐Antón G. Phylin 2.0: Extending the phylogeographical interpolation method to include uncertainty and user‐defined distance metrics. Mol Ecol Resour 2019; 19:1081-1094. [DOI: 10.1111/1755-0998.13010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 02/18/2019] [Accepted: 03/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Pedro Tarroso
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Sílvia B. Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo‐Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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25
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Mulder KP, Cortes‐Rodriguez N, Campbell Grant EH, Brand A, Fleischer RC. North-facing slopes and elevation shape asymmetric genetic structure in the range-restricted salamander Plethodon shenandoah. Ecol Evol 2019; 9:5094-5105. [PMID: 31110664 PMCID: PMC6509443 DOI: 10.1002/ece3.5064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/17/2019] [Accepted: 02/27/2019] [Indexed: 12/28/2022] Open
Abstract
Species with narrow environmental tolerances are often distributed within fragmented patches of suitable habitat, and dispersal among these subpopulations can be difficult to directly observe. Genetic data can help quantify gene flow between localities, which is especially important for vulnerable species with a disjunct range. The Shenandoah salamander (Plethodon shenandoah) is a federally endangered species known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture from individuals collected across all three mountaintops. Applying population and landscape genetic methods, we found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genomes indicated a deep split between the most southern population and the genetically similar central and northern populations. Although there was some mitochondrial haplotype-splitting between the central and northern populations, there was admixture in nuclear markers. This is indicative of either a recent split or current male-biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north-facing slopes at mid-elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of incorporating landscape features in understanding and predicting the movement and fragmentation of this range-restricted salamander species across space.
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Affiliation(s)
- Kevin P. Mulder
- Center for Conservation Genomics, National Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
- Research Center in Biodiversity and Genetic ResourcesCIBIO/InBIOVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
- Department of Vertebrate Zoology, National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Nandadevi Cortes‐Rodriguez
- Center for Conservation Genomics, National Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
- Department of BiologyIthaca CollegeIthacaNew York
| | - Evan H. Campbell Grant
- United States Geological Survey, Patuxent Wildlife Research CenterSO Conte Anadromous Fish Research LabTurners FallsMassachusetts
| | - Adrianne Brand
- United States Geological Survey, Patuxent Wildlife Research CenterSO Conte Anadromous Fish Research LabTurners FallsMassachusetts
| | - Robert C. Fleischer
- Center for Conservation Genomics, National Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
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26
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Ahmadi M, Hemami MR, Kaboli M, Malekian M, Zimmermann NE. Extinction risks of a Mediterranean neo-endemism complex of mountain vipers triggered by climate change. Sci Rep 2019; 9:6332. [PMID: 31004118 PMCID: PMC6474857 DOI: 10.1038/s41598-019-42792-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/04/2019] [Indexed: 01/13/2023] Open
Abstract
Climate change is among the most important drivers of biodiversity decline through shift or shrinkage in suitable habitat of species. Mountain vipers of the genus Montivipera are under extreme risk from climate changes given their evolutionary history and geographic distribution. In this study, we divided all Montivipera species into three phylogenetic-geographic Montivipera clades (PGMC; Bornmuelleri, Raddei and Xanthina) and applied an ensemble ecological niche modelling (ENM) approach under different climatic scenarios to assess changes in projected suitable habitats of these species. Based on the predicted range losses, we assessed the projected extinction risk of the species relative to IUCN Red List Criteria. Our result revealed a strong decline in suitable habitats for all PGMCs (63.8%, 79.3% and 96.8% for Xanthina, Raddei and Bornmuelleri, respectively, by 2070 and under 8.5 RCP scenario) with patterns of altitudinal range shifts in response to projected climate change. We found that the mountains close to the Mediterranean Sea are exposed to the highest threats in the future (84.6 ± 9.1 percent range loss). We also revealed that disjunct populations of Montivipera will be additionally highly isolated and fragmented in the future. We argue that leveraging climate niche projections into the risk assessment provides the opportunity to implement IUCN criteria and better assess forthcoming extinction risks of species.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Natural Resources, Isfahan University of Technology, Isfahan, 8415683111, Iran
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, 8415683111, Iran.
| | - Mohammad Kaboli
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Mansoureh Malekian
- Department of Natural Resources, Isfahan University of Technology, Isfahan, 8415683111, Iran
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27
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Dickson BG, Albano CM, Anantharaman R, Beier P, Fargione J, Graves TA, Gray ME, Hall KR, Lawler JJ, Leonard PB, Littlefield CE, McClure ML, Novembre J, Schloss CA, Schumaker NH, Shah VB, Theobald DM. Circuit-theory applications to connectivity science and conservation. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:239-249. [PMID: 30311266 PMCID: PMC6727660 DOI: 10.1111/cobi.13230] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 09/29/2018] [Accepted: 09/30/2018] [Indexed: 05/25/2023]
Abstract
Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least-cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open-source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat-use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.
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Affiliation(s)
- Brett G. Dickson
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
- Landscape Conservation Initiative, Northern Arizona University, Box 5694, Flagstaff, AZ, 86011, U.S.A
| | - Christine M. Albano
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
| | | | - Paul Beier
- School of Forestry, Northern Arizona University, Box 15018, Flagstaff, AZ, 86011, U.S.A
| | - Joe Fargione
- The Nature Conservancy – North America Region, 1101 West River Parkway, Suite 200, Minneapolis, MN, 55415, U.S.A
| | - Tabitha A. Graves
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 38 Mather Drive, West Glacier, MT, 59936, U.S.A
| | - Miranda E. Gray
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
| | - Kimberly R. Hall
- The Nature Conservancy – North America Region, 1101 West River Parkway, Suite 200, Minneapolis, MN, 55415, U.S.A
| | - Josh J. Lawler
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, U.S.A
| | - Paul B. Leonard
- U.S. Fish & Wildlife Service, Science Applications, 101 12th Avenue, Number 110, Fairbanks, AK, 99701, U.S.A
| | - Caitlin E. Littlefield
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, U.S.A
| | - Meredith L. McClure
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
| | - John Novembre
- Department of Human Genetics, Department of Ecology and Evolution, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, U.S.A
| | - Carrie A. Schloss
- The Nature Conservancy, 201 Mission Street, San Francisco, CA, 94105, U.S.A
| | - Nathan H. Schumaker
- U.S. Environmental Protection Agency, 200 Southwest 35th Street, Corvallis, OR, 97330, U.S.A
| | - Viral B. Shah
- Julia Computing, 45 Prospect Street, Cambridge, MA, 02139, U.S.A
| | - David M. Theobald
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
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28
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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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29
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Monteiro WP, Veiga JC, Silva AR, Carvalho CDS, Lanes ÉCM, Rico Y, Jaffé R. Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask). PeerJ 2019; 7:e6446. [PMID: 30783576 PMCID: PMC6377592 DOI: 10.7717/peerj.6446] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/15/2019] [Indexed: 11/30/2022] Open
Abstract
The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.
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Affiliation(s)
| | - Jamille Costa Veiga
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Amanda Reis Silva
- Departamento de Botânica, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | | | | | - Yessica Rico
- CONACYT, Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Michoacán, Mexico
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, PA, Brazil.,Departamento de Ecologia, Universidade de São Paulo, São Paulo, Brazil
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30
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Martins K, Gugger PF, Llanderal‐Mendoza J, González‐Rodríguez A, Fitz‐Gibbon ST, Zhao J, Rodríguez‐Correa H, Oyama K, Sork VL. Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa. Evol Appl 2018; 11:1842-1858. [PMID: 30459833 PMCID: PMC6231481 DOI: 10.1111/eva.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 05/31/2018] [Accepted: 07/11/2018] [Indexed: 12/30/2022] Open
Abstract
Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to non-native habitat and results in species-wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under future climate as a tool for forest restoration or management of the widely distributed high-elevation oak species Quercus rugosa in Mexico. Using genotyping by sequencing, we identified 5,354 single nucleotide polymorphisms (SNPs) genotyped from 103 individuals across 17 sites in the Trans-Mexican Volcanic Belt, and, after controlling for neutral genetic structure, we detected 74 F ST outlier SNPs and 97 SNPs associated with climate variation. Then, we deployed a nonlinear multivariate model, Gradient Forests, to map turnover in allele frequencies along environmental gradients and predict areas most sensitive to climate change. We found that spatial patterns of genetic variation were most strongly associated with precipitation seasonality and geographic distance. We identified regions of contemporary genetic and climatic similarities and predicted regions where future populations of Q. rugosa might be at risk due to high expected rate of climate change. Our findings provide preliminary details for future management strategies of Q. rugosa in Mexico and also illustrate how a landscape genomic approach can provide a useful tool for conservation and resource management strategies.
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Affiliation(s)
- Karina Martins
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Departamento de BiologiaUniversidade Federal de São CarlosSorocabaSPBrazil
| | - Paul F. Gugger
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMaryland
| | - Jesus Llanderal‐Mendoza
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
- Escuela Nacional de Estudios Superiores Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Antonio González‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Sorel T. Fitz‐Gibbon
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
| | - Jian‐Li Zhao
- Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnanChina
| | - Hernando Rodríguez‐Correa
- Escuela Nacional de Estudios Superiores Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Victoria L. Sork
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Institute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCalifornia
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31
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Fine-scale genetic structure in a salamander with two reproductive modes: Does reproductive mode affect dispersal? Evol Ecol 2018. [DOI: 10.1007/s10682-018-9957-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Combining phylogeography and landscape genetics to infer the evolutionary history of a short-range Mediterranean relict, Salamandra salamandra longirostris. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1110-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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GonÇalves DV, Pereira P, Velo-AntÓn G, Harris DJ, Carranza S, Brito JC. Assessing the role of aridity-induced vicariance and ecological divergence in species diversification in North-West Africa using Agama lizards. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Duarte V GonÇalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, Porto, Portugal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Paulo Pereira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, Porto, Portugal
| | - Guillermo Velo-AntÓn
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - D James Harris
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, Porto, Portugal
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - JosÉ C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, Porto, Portugal
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34
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Phylogeography of the Japanese ratsnake, Elaphe climacophora (Serpentes: Colubridae): impacts of Pleistocene climatic oscillations and sea-level fluctuations on geographical range. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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35
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Phylogenomic insights into the diversification of salamanders in the Isthmura bellii group across the Mexican highlands. Mol Phylogenet Evol 2018; 125:78-84. [PMID: 29555294 DOI: 10.1016/j.ympev.2018.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/10/2018] [Accepted: 03/15/2018] [Indexed: 11/22/2022]
Abstract
Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity.
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36
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Martínez-Freiría F, Crochet PA, Fahd S, Geniez P, Brito JC, Velo-Antón G. Integrative phylogeographical and ecological analysis reveals multiple Pleistocene refugia for Mediterranean Daboia vipers in north-west Africa. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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37
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Model-based analyses reveal insular population diversification and cryptic frog species in the Ischnocnema parva complex in the Atlantic forest of Brazil. Mol Phylogenet Evol 2017; 112:68-78. [DOI: 10.1016/j.ympev.2017.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 11/18/2022]
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38
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Rovito SM, Schoville SD. Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders. Heredity (Edinb) 2017. [PMID: 28635966 DOI: 10.1038/hdy.2017.31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Pleistocene glaciations have profoundly affected patterns of genetic diversity within many species. Temperate alpine organisms likely experienced dramatic range shifts, given that much of their habitat was glaciated during this time. While the effects of glaciations are relatively well understood, the spatial locations of refugia and processes that gave rise to current patterns of diversity are less well known. We use a microsatellite data set to test hypotheses of population connectivity and refugial isolation in the web-toed salamanders (Hydromantes) of the Sierra Nevada. We reject models of refugia with subsequent expansion into either the high southern Sierra or low-elevation Owens Valley, in favor of a simple isolation model with no migration between current populations. We find no evidence of migration at even moderate spatial scales using a variety of analyses in the southern Sierra, and limited migration in the northern Sierra. These results suggest that divergence in isolation following fragmentation is the dominant process structuring genetic variation in these salamander species. In the context of anthropogenic climate change and habitat degradation, these results imply that salamanders and other low-vagility alpine organisms are at risk of decline as they are unlikely to migrate across large distances.
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Affiliation(s)
- S M Rovito
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
| | - S D Schoville
- Université Joseph Fourier, Grenoble, Centre National de la Recherche Scientifique TIMC-IMAG UMR 5525, Equipe Biologie Computationnelle et Mathématique, Grenoble, France.,Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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39
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Noguerales V, Cordero PJ, Ortego J. Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper. Ecol Evol 2017; 7:3110-3122. [PMID: 28480010 PMCID: PMC5415511 DOI: 10.1002/ece3.2810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/31/2016] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Understanding the processes underlying spatial patterns of genetic diversity and structure of natural populations is a central topic in evolutionary biogeography. In this study, we combine data on ancient and contemporary landscape composition to get a comprehensive view of the factors shaping genetic variation across the populations of the scrub‐legume grasshopper (Chorthippus binotatus binotatus) from the biogeographically complex region of southeast Iberia. First, we examined geographical patterns of genetic structure and employed an approximate Bayesian computation (ABC) approach to compare different plausible scenarios of population divergence. Second, we used a landscape genetic framework to test for the effects of (1) Late Miocene paleogeography, (2) Pleistocene climate fluctuations, and (3) contemporary topographic complexity on the spatial patterns of population genetic differentiation. Genetic structure and ABC analyses supported the presence of three genetic clusters and a sequential west‐to‐east splitting model that predated the last glacial maximum (LGM, c. 21 Kya). Landscape genetic analyses revealed that population genetic differentiation was primarily shaped by contemporary topographic complexity, but was not explained by any paleogeographic scenario or resistance distances based on climate suitability in the present or during the LGM. Overall, this study emphasizes the need of integrating information on ancient and contemporary landscape composition to get a comprehensive view of their relative importance to explain spatial patterns of genetic variation in organisms inhabiting regions with complex biogeographical histories.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
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40
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Angulo DF, Amarilla LD, Anton AM, Sosa V. Colonization in North American Arid Lands: The Journey of Agarito (Berberis trifoliolata) Revealed by Multilocus Molecular Data and Packrat Midden Fossil Remains. PLoS One 2017; 12:e0168933. [PMID: 28146559 PMCID: PMC5287450 DOI: 10.1371/journal.pone.0168933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
Here we conduct research to understand the evolutionary history of a shrubby species known as Agarito (Berberis trifoliolata), an endemic species to the Chihuahuan Desert. We identify genetic signatures based on plastid DNA and AFLP markers and perform niche modelling and spatial connectivity analyses as well as niche modelling based on records in packrats to elucidate whether orogenic events such as mountain range uplift in the Miocene or the contraction/expansion dynamics of vegetation in response to climate oscillations in the Pliocene/Pleistocene had an effect on evolutionary processes in Agarito. Our results of current niche modelling and palaeomodelling showed that the area currently occupied by Berberis trifoliolata is substantially larger than it was during the Last Interglacial period and the Last Glacial Maximum. Agarito was probably confined to small areas in the Northeastern and gradually expanded its distribution just after the Last Glacial Maximum when the weather in the Chihuahuan Desert and adjacent regions became progressively warmer and drier. The most contracted range was predicted for the Interglacial period. Populations remained in stable areas during the Last Glacial Maximum and expanded at the beginning of the Holocene. Most genetic variation occured in populations from the Sierra Madre Oriental. Two groups of haplotypes were identified: the Mexican Plateau populations and certain Northeastern populations. Haplogroups were spatially connected during the Last Glacial Maximum and separated during interglacial periods. The most important prediction of packrat middens palaeomodelling lies in the Mexican Plateau, a finding congruent with current and past niche modelling predictions for agarito and genetic results. Our results corroborate that these climate changes in the Pliocene/Pleistocene affected the evolutionary history of agarito. The journey of agarito in the Chihuahuan Desert has been dynamic, expanding and contracting its distribution range and currently occupying the largest area in its history.
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Affiliation(s)
- Diego F Angulo
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Leonardo D Amarilla
- Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ana M Anton
- Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Victoria Sosa
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
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41
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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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42
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Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species. PLoS One 2016; 11:e0169165. [PMID: 28033364 PMCID: PMC5199109 DOI: 10.1371/journal.pone.0169165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/13/2016] [Indexed: 11/19/2022] Open
Abstract
Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.
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43
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Zarza E, Faircloth BC, Tsai WL, Bryson RW, Klicka J, McCormack JE. Hidden histories of gene flow in highland birds revealed with genomic markers. Mol Ecol 2016; 25:5144-5157. [DOI: 10.1111/mec.13813] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Eugenia Zarza
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Whitney L.E. Tsai
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Robert W. Bryson
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John E. McCormack
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
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44
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Noguerales V, Cordero PJ, Ortego J. Hierarchical genetic structure shaped by topography in a narrow-endemic montane grasshopper. BMC Evol Biol 2016; 16:96. [PMID: 27149952 PMCID: PMC4858822 DOI: 10.1186/s12862-016-0663-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Understanding the underlying processes shaping spatial patterns of genetic structure in free-ranging organisms is a central topic in evolutionary biology. Here, we aim to disentangle the relative importance of neutral (i.e. genetic drift) and local adaptation (i.e. ecological divergence) processes in the evolution of spatial genetic structure of the Morales grasshopper (Chorthippus saulcyi moralesi), a narrow-endemic taxon restricted to the Central Pyrenees. More specifically, we analysed range-wide patterns of genetic structure and tested whether they were shaped by geography (isolation-by-distance, IBD), topographic complexity and present and past habitat suitability models (isolation-by-resistance, IBR), and environmental dissimilarity (isolation-by-environment, IBE). RESULTS Different clustering analyses revealed a deep genetic structure that was best explained by IBR based on topographic complexity. Our analyses did not reveal a significant role of IBE, a fact that may be due to low environmental variation among populations and/or consequence of other ecological factors not considered in this study are involved in local adaptation processes. IBR scenarios informed by current and past climate distribution models did not show either a significant impact on genetic differentiation after controlling for the effects of topographic complexity, which may indicate that they are not capturing well microhabitat structure in the present or the genetic signal left by dispersal routes defined by habitat corridors in the past. CONCLUSIONS Overall, these results indicate that spatial patterns of genetic variation in our study system are primarily explained by neutral divergence and migration-drift equilibrium due to limited dispersal across abrupt reliefs, whereas environmental variation or spatial heterogeneity in habitat suitability associated with the complex topography of the region had no significant effect on genetic discontinuities after controlling for geography. Our study highlights the importance of considering a comprehensive suite of potential isolating mechanisms and analytical approaches in order to get robust inferences on the processes promoting genetic divergence of natural populations.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071, Ciudad Real, Spain.
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071, Ciudad Real, Spain
| | - Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio s/n, E-41092, Seville, Spain
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Watts AG, Schlichting PE, Billerman SM, Jesmer BR, Micheletti S, Fortin MJ, Funk WC, Hapeman P, Muths E, Murphy MA. How spatio-temporal habitat connectivity affects amphibian genetic structure. Front Genet 2015; 6:275. [PMID: 26442094 PMCID: PMC4561841 DOI: 10.3389/fgene.2015.00275] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/14/2015] [Indexed: 11/13/2022] Open
Abstract
Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.
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Affiliation(s)
- Alexander G Watts
- Department of Ecology & Evolutionary Biology, University of Toronto Toronto, ON, Canada
| | - Peter E Schlichting
- Department of Natural Resources Management, Texas Tech University Lubbock, TX, USA
| | - Shawn M Billerman
- Department of Zoology and Physiology, University of Wyoming Laramie, WY, USA ; Program in Ecology, University of Wyoming Laramie, WY, USA
| | - Brett R Jesmer
- Department of Zoology and Physiology, University of Wyoming Laramie, WY, USA ; Program in Ecology, University of Wyoming Laramie, WY, USA
| | - Steven Micheletti
- School of Biological Sciences, Washington State University Pullman, WA, USA
| | - Marie-Josée Fortin
- Department of Ecology & Evolutionary Biology, University of Toronto Toronto, ON, Canada
| | - W Chris Funk
- Graduate Degree Program in Ecology, Department of Biology, Colorado State University Fort Collins, CO, USA
| | - Paul Hapeman
- Department of Biology, Central Connecticut State University New Britain, CT, USA
| | - Erin Muths
- Fort Collins Science Center, U.S. Geological Survey Fort Collins, CO, USA
| | - Melanie A Murphy
- Program in Ecology, University of Wyoming Laramie, WY, USA ; Department of Ecosystem Science and Management, University of Wyoming Laramie, WY, USA
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Gonçalves H, Maia-Carvalho B, Sousa-Neves T, García-París M, Sequeira F, Ferrand N, Martínez-Solano I. Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium. Mol Phylogenet Evol 2015; 93:363-79. [PMID: 26282950 DOI: 10.1016/j.ympev.2015.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
Recent investigations on the evolutionary history of the common midwife toad (Alytes obstetricans) revealed high levels of geographically structured genetic diversity but also a situation where delineation of major historical lineages and resolution of their relationships are much more complex than previously thought. We studied sequence variation in one mitochondrial and four nuclear genes throughout the entire distribution range of all recognized A. obstetricans subspecies to infer the evolutionary processes that shaped current patterns of genetic diversity and population subdivision. We found six divergent, geographically structured mtDNA haplogroups diagnosing population lineages, and varying levels of admixture in nuclear markers. Given the timeframe inferred for the splits between major lineages, the climatic and environmental changes that occurred during the Pleistocene seem to have shaped the diversification history of A. obstetricans. Survival of populations in allopatric refugia through the Ice Ages supports the generality of the "refugia-within-refugia" scenario for the Iberian Peninsula. However, lineages corresponding to subspecies A. o. almogavarii, A. o. pertinax, A. o. obstetricans, and A. o. boscai responded differently to Pleistocene climatic oscillations after diverging from a common ancestor. Alytes o. obstetricans expanded northward from a northern Iberian refugium through the western Pyrenees, leaving a signal of contrasting patterns of genetic diversity, with a single mtDNA haplotype north of the Pyrenees from SW France to Germany. Both A. o. pertinax and A. o. boscai are widespread and genetically diverse in Iberia, the latter comprising two divergent lineages with a long independent history. Finally, A. o. almogavarii is mostly restricted to the north-eastern corner of Iberia north of the Ebro river, with additional populations in a small region in south-eastern France. This taxon exhibits unparalleled levels of genetic diversity and little haplotype sharing with other lineages, suggesting a process of incipient speciation.
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Affiliation(s)
- H Gonçalves
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - B Maia-Carvalho
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal
| | - T Sousa-Neves
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Museu Paraense Emílio Goeldi, Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - M García-París
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - F Sequeira
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - N Ferrand
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal; Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - I Martínez-Solano
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, s/n, 13005 Ciudad Real, Spain; Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio, s/n, 41092 Sevilla, Spain
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Nowakowski AJ, Veiman-Echeverria M, Kurz DJ, Donnelly MA. Evaluating connectivity for tropical amphibians using empirically derived resistance surfaces. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:928-942. [PMID: 26465034 DOI: 10.1890/14-0833.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Agricultural expansion continues to drive forest loss in species-rich tropical systems and often disrupts movement and distributions of organisms. The ability of species to occupy and move through altered habitats likely depends on the level of contrast between natural forest and surrounding land uses. Connectivity models, such as circuit theory models, are widely used in conservation biology, and their primary input consists of resistance surfaces representing movement costs associated with landscape features. Cost values are most frequently determined by expert opinion, which may not capture relevant levels of contrast among features. We developed resistance surfaces using experiments that represent different local mechanisms hypothesized to affect connectivity for two Neotropical amphibian species. Response ratios were calculated to translate experimental results to cost values used in connectivity modeling. We used relative abundance data in three land-cover types to generate resistance surfaces for evaluating independent support of models derived from experiments. Finally, we analyzed agreement among movement pathways predicted for each species and among three commonly used connectivity measures: Euclidean, least cost, and resistance distances. Experiments showed that extreme microclimates associated with altered habitats significantly increased desiccation and mortality risk for both species. Resistances estimated from microclimate experiments were concordant with those from survey data for both species. For one focal species, resistance estimates derived from predator encounter rates were also highly correlated with abundance-derived resistances. There was generally low agreement among the three alternative distance measures, which underscores the importance of choosing connectivity models that are most appropriate for the study objectives. Overall, similarity among linkages modeled for each species was high, but decreased with declining forest cover. Our results highlight the value of experiments for drawing inferences about processes in resistance modeling, as well as the need to consider model differences and species-specific responses when developing strategies to maintain connectivity.
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Damasceno R, Strangas ML, Carnaval AC, Rodrigues MT, Moritz C. Revisiting the vanishing refuge model of diversification. Front Genet 2014; 5:353. [PMID: 25374581 PMCID: PMC4205810 DOI: 10.3389/fgene.2014.00353] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/21/2014] [Indexed: 11/13/2022] Open
Abstract
Much of the debate around speciation and historical biogeography has focused on the role of stabilizing selection on the physiological (abiotic) niche, emphasizing how isolation and vicariance, when associated with niche conservatism, may drive tropical speciation. Yet, recent re-emphasis on the ecological dimensions of speciation points to a more prominent role of divergent selection in driving genetic, phenotypic, and niche divergence. The vanishing refuge model (VRM), first described by Vanzolini and Williams (1981), describes a process of diversification through climate-driven habitat fragmentation and exposure to new environments, integrating both vicariance and divergent selection. This model suggests that dynamic climates and peripheral isolates can lead to genetic and functional (i.e., ecological and phenotypic) diversity, resulting in sister taxa that occupy contrasting habitats with abutting distributions. Here, we provide predictions for populations undergoing divergence according to the VRM that encompass habitat dynamics, phylogeography, and phenotypic differentiation across populations. Such integrative analyses can, in principle, differentiate the operation of the VRM from other speciation models. We applied these principles to a lizard species, Coleodactylus meridionalis, which was used to illustrate the model in the original paper. We incorporate data on inferred historic habitat dynamics, phylogeography and thermal physiology to test for divergence between coastal and inland populations in the Atlantic Forest of Brazil. Environmental and genetic analyses are concordant with divergence through the VRM, yet physiological data are not. We emphasize the importance of multidisciplinary approaches to test this and alternative speciation models while seeking to explain the extraordinarily high genetic and phenotypic diversity of tropical biomes.
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Affiliation(s)
- Roberta Damasceno
- Museum of Vertebrate Zoology, Integrative Biology Department, University of California Berkeley Berkeley, CA, USA ; Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo São Paulo, Brazil
| | - Maria L Strangas
- Biology Department, The Graduate Center, City University of New York New York, NY, USA
| | - Ana C Carnaval
- Biology Department, The Graduate Center, City University of New York New York, NY, USA ; Biology Department, City College, City University of New York New York, NY, USA
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo São Paulo, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, Integrative Biology Department, University of California Berkeley Berkeley, CA, USA ; Research School of Biology, The Australian National University Acton, ACT, Australia
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Zancolli G, Rödel MO, Steffan-Dewenter I, Storfer A. Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro. Mol Ecol 2014; 23:4989-5002. [DOI: 10.1111/mec.12921] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 09/07/2014] [Accepted: 09/10/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Giulia Zancolli
- Department of Animal Ecology and Tropical Biology; Biocentre; University of Würzburg; Am Hubland 97074 Würzburg Germany
- School of Biological Sciences; Washington State University; Pullman WA 99164 USA
| | - Mark-Oliver Rödel
- Museum für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; Invalidenstr. 43 10115 Berlin Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB); Berlin Germany
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology; Biocentre; University of Würzburg; Am Hubland 97074 Würzburg Germany
| | - Andrew Storfer
- School of Biological Sciences; Washington State University; Pullman WA 99164 USA
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50
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Martínez-Freiría F, Velo-Antón G, Brito JC. Trapped by climate: interglacial refuge and recent population expansion in the endemic Iberian adderVipera seoanei. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12265] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Fernando Martínez-Freiría
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - José C. Brito
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Instituto de Ciências Agrárias de Vairão; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
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