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Nottingham S, Pelletier TA. The impact of climate change on western Plethodon salamanders' distribution. Ecol Evol 2021; 11:9370-9384. [PMID: 34306628 PMCID: PMC8293714 DOI: 10.1002/ece3.7735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
AIM Given that salamanders have experienced large shifts in their distributions over time, we determined how each species of Plethodon in the Pacific Northwest would respond to climate change. We incorporated several greenhouse scenarios both on a species-by-species basis, and also using phylogenetic groups, with the aim to determine the best course of action in managing land area to conserve diversity in this group. LOCATION Pacific Northwest of the United States (northern CA, OR, WA, ID, and MT). MAJOR TAXA STUDIED Western Plethodon salamanders. METHODS Species distribution models were estimated using MaxEnt for the current time period and for several future climate scenarios using bioclimatic data layers. We used several methods to quantify the change in habitat suitability over time from the models. We explored aspects of the climate layers to determine whether we can expect a concerted response to climate change due to similarity in ecological niche or independent responses that could be harder to manage. RESULTS The distribution of western Plethodon salamander species is strongly influenced by precipitation and less so by temperature. Species responses to climate change resulted in both increases and decreases in predicted suitable habitat, though most species ranges do not contract, especially when taken as a phylogenetic group. MAIN CONCLUSIONS While some established habitats may become more or less climatically suitable, the overall distribution of species in this group is unlikely to be significantly affected. Clades of Plethodon species are unlikely to be in danger of extirpation despite the possibility that individual species may be threatened as a result of limited distributions. Grouping species into lineages with similar geographic ranges can be a viable method of determining conservation needs. More biotic and dispersal information is needed to determine the true impact that changes in climate will have on the distribution of Plethodon species.
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Costanzi JM, Mège P, Boissinot A, Isselin-Nondedeu F, Guérin S, Lourdais O, Trochet A, Le Petitcorps Q, Legrand A, Varenne F, Grillet P, Morin-Pinaud S, Picard D. Agricultural landscapes and the Loire River influence the genetic structure of the marbled newt in Western France. Sci Rep 2018; 8:14177. [PMID: 30242196 PMCID: PMC6155057 DOI: 10.1038/s41598-018-32514-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/10/2018] [Indexed: 11/26/2022] Open
Abstract
Amphibians are particularly sensitive to landscape fragmentation. Potential barriers between breeding sites can negatively influence the dispersal of individuals and increase genetic structure between populations. In this study, we genotyped 10 microsatellites for 334 marbled newts (Triturus marmoratus) at 11 different locations in Western France. Samples were collected in different regions with contrasting agricultural landscapes (low and high proportion of arable land in the north and south, respectively). We found a strong genetic structure between the northern and southern sampling sites. Isolation by distance was recorded after 62 km, but within the northern region, little or no genetic structure was detected over large distances (up to 114 km). Genetic structure at shorter distance (43 km) was found between sites situated in landscapes with larger amounts of arable lands. A significant positive relationship was found between the pairwise genetic distance (Fst) between sites and the amount of arable land together with the distance between sites. Our results suggest that the Loire River might act as a corridor for the marbled newt, while arable land might act as a barrier. Finally, although a large city is located between sampling sites, no effect was detected on population structure.
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Affiliation(s)
- Jean-Marc Costanzi
- Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway, Gullbringvegen 36, Bø i Telemark, 3800, Norway.
| | - Pascal Mège
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
| | - Alexandre Boissinot
- Centre d'Études Biologiques de Chizé, CNRS et Université de la Rochelle - UMR 7372, F-79360, Villiers en Bois, France
| | - Francis Isselin-Nondedeu
- Ecole Polytechnique de l'Université François Rabelais, Département d'Aménagement et d'Environnement, UMR 7324 - CNRS CITERES 33-35 allée Ferdinand de Lesseps, 37200, Tours, France
- IMBE, UMR Université Aix-Marseille Avignon, 7223-CNRS, 237-IRD IRPNC (Ingénierie de la Restauration des Patrimoines Naturels et Culturels), Avignon, France
| | - Sandra Guérin
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
- EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, F-34293, Montpellier, France
| | - Olivier Lourdais
- Centre d'Études Biologiques de Chizé, CNRS et Université de la Rochelle - UMR 7372, F-79360, Villiers en Bois, France
| | - Audrey Trochet
- CNRS, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, Toulouse, F-31062, France
- Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, F-09200, France
| | - Quentin Le Petitcorps
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
| | - Agathe Legrand
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
| | | | | | - Sophie Morin-Pinaud
- Office National de la Chasse et de la Faune Sauvage - Unité Avifaune migratrice, Direction de la Recherche et de l'Expertise, F-79360, Villiers en Bois, France
| | - Damien Picard
- Département de Biologie, UFR de Sciences, Université d'Angers, 2 Boulevard de Lavoisier, 49000, Angers, France
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Pelletier TA, Crisafulli C, Wagner S, Zellmer AJ, Carstens BC. Historical Species Distribution Models Predict Species Limits in WesternPlethodonSalamanders. Syst Biol 2014; 64:909-25. [DOI: 10.1093/sysbio/syu090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/10/2014] [Indexed: 11/12/2022] Open
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Matala AP, Ackerman MW, Campbell MR, Narum SR. Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes. Evol Appl 2014; 7:682-701. [PMID: 25067950 PMCID: PMC4105918 DOI: 10.1111/eva.12174] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 05/06/2014] [Indexed: 12/25/2022] Open
Abstract
Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species.
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Affiliation(s)
- Andrew P Matala
- Columbia River Inter-Tribal Fish Commission Hagerman, ID, USA
| | - Michael W Ackerman
- Eagle Fish Genetic Laboratory, Pacific States Marine Fisheries Commission Eagle, ID, USA
| | - Matthew R Campbell
- Eagle Fish Genetic Laboratory, Idaho Department of Fish and Game Eagle, ID, USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission Hagerman, ID, USA
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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Pelletier TA, Duffield DA, DeGrauw EA. Rangewide Phylogeography of the Western Red-Backed Salamander (Plethodon vehiculum). ACTA ACUST UNITED AC 2011. [DOI: 10.1898/10-23.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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Lee-Yaw JA, Irwin JT, Green DM. Postglacial range expansion from northern refugia by the wood frog, Rana sylvatica. Mol Ecol 2007; 17:867-84. [PMID: 18179428 DOI: 10.1111/j.1365-294x.2007.03611.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the range dynamics of North American amphibians during the last glacial cycle are increasingly better understood, the recolonization history of the most northern regions and the impact of southern refugia on patterns of intraspecific genetic diversity and phenotypic variation in these regions are not well reconstructed. Here we present the phylogeographic history of a widespread and primarily northern frog, Rana sylvatica. We surveyed 551 individuals from 116 localities across the species' range for a 650-bp region of the NADH dehydrogenase subunit 2 and tRNA(TRP) mitochondrial genes. Our phylogenetic analyses revealed two distinct clades corresponding to eastern and western populations, as well as a Maritime subclade within the eastern lineage. Patterns of genetic diversity support multiple refugia. However, high-latitude refugia in the Appalachian highlands and modern-day Wisconsin appear to have had the biggest impact on northern populations. Clustering analyses based on morphology further support a distinction between eastern and western wood frogs and suggest that postglacial migration has played an important role in generating broad-scale patterns of phenotypic variation in this species.
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Affiliation(s)
- Julie A Lee-Yaw
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, QC, Canada.
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Marsh D, Page R, Hanlon T, Bareke H, Corritone R, Jetter N, Beckman N, Gardner K, Seifert D, Cabe P. Ecological and genetic evidence that low-order streams inhibit dispersal by red-backed salamanders (Plethodon cinereus). CAN J ZOOL 2007. [DOI: 10.1139/z07-008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
While many studies have examined the barrier effects of large rivers on animal dispersal and gene flow, few studies have considered the barrier effects of small streams. We used displacement experiments and analyses of genetic population structure to examine the effects of first-order and second-order streams on the dispersal of terrestrial red-backed salamanders, Plethodon cinereus (Green, 1818). We marked red-backed salamanders from near the edges of one first-order stream and one second-order stream, and experimentally displaced them either across the stream or an equal distance farther into the forest. A comparison of return rates indicated that both streams were partial barriers to salamander movement, reducing return rates by approximately 50%. Analysis of six microsatellite loci from paired plots on the same side and on opposite sides of the second-order stream suggested that the stream did contribute to genetic differentiation of salamander populations. Collectively, our results imply that low-order streams do influence patterns of movement and gene flow in red-backed salamanders. We suggest that given the high density of first-order and second-order streams in most landscapes, these features may have important effects on species that, like red-backed salamanders, have limited dispersal and large geographic ranges.
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Affiliation(s)
- D.M. Marsh
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - R.B. Page
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - T.J. Hanlon
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - H. Bareke
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - R. Corritone
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - N. Jetter
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - N.G. Beckman
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - K. Gardner
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - D.E. Seifert
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
| | - P.R. Cabe
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
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Miller MP, Haig SM, Wagner RS. Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management. ACTA ACUST UNITED AC 2006; 97:561-70. [PMID: 17135462 DOI: 10.1093/jhered/esl038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.
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Affiliation(s)
- Mark P Miller
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
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Steele CA, Storfer A. Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Mol Ecol 2006; 15:2477-87. [PMID: 16842421 DOI: 10.1111/j.1365-294x.2006.02950.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.
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Affiliation(s)
- Craig A Steele
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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