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Antunes B, Figueiredo-Vázquez C, Dudek K, Liana M, Pabijan M, Zieliński P, Babik W. Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris). Mol Ecol 2023; 32:4515-4530. [PMID: 35593303 DOI: 10.1111/mec.16543] [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: 08/05/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
Ecologically distinct species may respond to landscape changes in different ways. In addition to basic ecological data, the extent of the geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species - the range-restricted, Lissotriton montandoni and the widespread, L. vulgaris - using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with L. montandoni and L. vulgaris showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in L. montandoni than in L. vulgaris. This result is consistent with a view of L. vulgaris as an ecological generalist. Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to L. montandoni. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.
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Affiliation(s)
- Bernardo Antunes
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Clara Figueiredo-Vázquez
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | - Maciej Pabijan
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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Martínez-Gil H, Sánchez-Montes G, Montes-Gavilán P, Ugarte G, Martínez-Solano Í. Fine-scale functional connectivity of two syntopic pond-breeding amphibians with contrasting life-history traits: an integrative assessment of direct and indirect estimates of dispersal. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01506-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
AbstractAssessing patterns of functional connectivity among amphibian demes is crucial to unravel their population dynamics and prevent their isolation and eventual extinction. Integrative studies based on direct (capture-mark-recapture) and indirect (genetic) estimates of dispersal provide robust, biologically realistic inferences on population structure and connectivity, with applications for conservation efforts. We focused on two pond-breeding amphibians with contrasting life-history traits: the short-lived, semi-arboreal Hyla molleri and the long-lived, fossorial Pelobates cultripes. We PIT-tagged 2150 individuals of both species in two ponds (Laguna and Gravera, separated by 700 m) and monitored them from 2009 to 2021 to document the frequency and spatial extent of dispersal events. In addition, we genotyped individuals from these and two additional breeding populations at a maximum distance of 5 km with 15–16 microsatellites to characterize fine-scale patterns of genetic structure. We detected dispersal events connecting Laguna and Gravera in both species, albeit at low frequencies (4.8% and 7.7% of recaptured individuals of H. molleri and P. cultripes, respectively). However, both species were capable of covering long distances, with individual accumulated displacements up to 3.5 km (Hyla) and 1.8 km (Pelobates). Breeding populations > 2 km apart were genetically differentiated, indicating lower connectivity at this spatial scale. Estimates of pairwise migration rates differed between species and were asymmetrical, with different ponds representing “source” populations contributing more migrants to other populations in each species. We discuss the role of differences in life history traits and ecological preferences in shaping population dynamics in the two species and highlight management implications of our results.
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Pröhl H, Auffarth J, Bergmann T, Buschmann H, Balkenhol N. Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure, genetic diversity and landscape effects in an endangered amphibian. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01350-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractRevealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.
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Reconciling direct and indirect estimates of functional connectivity in a Mediterranean pond-breeding amphibian. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01345-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Pabijan M, Palomar G, Antunes B, Antoł W, Zieliński P, Babik W. Evolutionary principles guiding amphibian conservation. Evol Appl 2020; 13:857-878. [PMID: 32431739 PMCID: PMC7232768 DOI: 10.1111/eva.12940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.
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Affiliation(s)
- Maciej Pabijan
- Institute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Gemma Palomar
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bernardo Antunes
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Weronika Antoł
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Wiesław Babik
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
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Ichikawa R, Toyoizumi R. Finely tuned ciliary alignment and coordinated beating generate continuous water flow across the external gills in Pleurodeles waltl larvae. ZOOMORPHOLOGY 2020. [DOI: 10.1007/s00435-020-00479-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Baden AL, Mancini AN, Federman S, Holmes SM, Johnson SE, Kamilar J, Louis EE, Bradley BJ. Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range. Sci Rep 2019; 9:16276. [PMID: 31700150 PMCID: PMC6838192 DOI: 10.1038/s41598-019-52689-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.
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Affiliation(s)
- Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, 10065, USA.
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA
| | - Sarah Federman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Sheila M Holmes
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Jason Kamilar
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, 01003, USA
| | - Edward E Louis
- Omaha's Henry Doorly Zoo and Aquarium, 3701S 10th St, Omaha, NE68107, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052, USA
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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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Cogne Y, Almunia C, Gouveia D, Pible O, François A, Degli-Esposti D, Geffard O, Armengaud J, Chaumot A. Comparative proteomics in the wild: Accounting for intrapopulation variability improves describing proteome response in a Gammarus pulex field population exposed to cadmium. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 214:105244. [PMID: 31352074 DOI: 10.1016/j.aquatox.2019.105244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/14/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
High-throughput proteomics can be performed on animal sentinels for discovering key molecular biomarkers signing the physiological response and adaptation of organisms. Ecotoxicoproteomics is today amenable by means of proteogenomics to small arthropods such as Gammarids which are well known sentinels of aquatic environments. Here, we analysed two regional Gammarus pulex populations to characterize the potential proteome divergence induced in one site by natural bioavailable mono-metallic contamination (cadmium) compared to a non-contaminated site. Two RNAseq-derived protein sequence databases were established previously on male and female individuals sampled from the reference site. Here, individual proteomes were acquired on 10 male and 10 female paired organisms sampled from each site. Proteins involved in protein lipidation, carbohydrate metabolism, proteolysis, innate immunity, oxidative stress response and lipid transport were found more abundant in animals exposed to cadmium, while hemocyanins were found in lower abundance. The intrapopulation proteome variability of long-term exposed G. pulex was inflated relatively to the non-contaminated population. These results show that, while remaining a challenge for such organisms with not yet sequenced genomes, taking into account intrapopulation variability is important to better define the molecular players induced by toxic stress in a comparative field proteomics approach.
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Affiliation(s)
- Yannick Cogne
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Christine Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Adeline François
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Davide Degli-Esposti
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Geffard
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France.
| | - Arnaud Chaumot
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
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Emel SL, Olson DH, Knowles LL, Storfer A. Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus: implications for forest management and species conservation. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01172-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Phylogeography of Atlantic Forest glassfrogs (Vitreorana): when geography, climate dynamics and rivers matter. Heredity (Edinb) 2018; 122:545-557. [PMID: 30356224 DOI: 10.1038/s41437-018-0155-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/10/2018] [Accepted: 09/25/2018] [Indexed: 11/08/2022] Open
Abstract
Recent advances in the field of landscape genetics provide ways to jointly analyze the role of present-day climate and landscape configuration in current biodiversity patterns. Expanding this framework into a phylogeographic study, we incorporate information on historical climatic shifts, tied to descriptions of the local topography and river configuration, to explore the processes that underlie genetic diversity patterns in the Atlantic Forest hotspot. We study two montane, stream-associated species of glassfrogs: Vitreorana eurygnatha and V. uranoscopa. By integrating species distribution modeling with geographic information systems and molecular data, we find that regional patterns of molecular diversity are jointly explained by geographic distance, historical (last 120 ky) climatic stability, and (in one species) river configuration. Mitochondrial DNA genealogies recover significant regional structure in both species, matching previous classifications of the northern and southern forests in the Atlantic Forest, and are consistent with patterns reported in other taxa. Yet, these spatial patterns of genetic diversity are only partially supported by nuclear data. Contrary to data from lowland taxa, historical climate projections suggest that these montane species were able to persist in the southern Atlantic Forest during glacial periods, particularly during the Last Glacial Maximum. These results support generally differential responses to climatic cycling by northern (lowland) and southern (montane) Atlantic Forest species, triggered by the joint impact of regional landscape configuration and climate change.
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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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Gutiérrez-Rodríguez J, Sánchez-Montes G, Martínez-Solano I. Effective to census population size ratios in two Near Threatened Mediterranean amphibians: Pleurodeles waltl and Pelobates cultripes. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0971-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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