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Maier PA, Vandergast AG, Bohonak AJ. Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad ( Anaxyrus canorus). Evol Appl 2023; 16:74-97. [PMID: 36699123 PMCID: PMC9850018 DOI: 10.1111/eva.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/05/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future "Geminate Evolutionary Units" (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo-genomic simulations. Using this process, we delineated conservation units for the Yosemite toad (Anaxyrus canorus), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome-wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection (R 2 ranging from 0.09 to 0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF-North (high winter snowpack with moderate summer rainfall), YF-East (low to moderate snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF-East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, and (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non-model species with genomic data alone and has wide applicability to other declining species.
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Affiliation(s)
- Paul A. Maier
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
- FamilyTreeDNAGene by GeneHoustonTexasUSA
| | - Amy G. Vandergast
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCaliforniaUSA
| | - Andrew J. Bohonak
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Landscape genetics of a sub-alpine toad: climate change predicted to induce upward range shifts via asymmetrical migration corridors. Heredity (Edinb) 2022; 129:257-272. [PMID: 36076071 PMCID: PMC9613655 DOI: 10.1038/s41437-022-00561-x] [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: 05/16/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.
- FamilyTreeDNA, Gene by Gene, 1445 N Loop W, Houston, TX, 77008, USA.
| | - Amy G Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, CA, 92101, USA
| | - Steven M Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the Environment, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Dr., Los Angeles, CA, 90032, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
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Balantic C, Adams A, Gross S, Mazur R, Sawyer S, Tucker J, Vernon M, Mengelt C, Morales J, Thorne JH, Brown TM, Athearn N, Morelli TL. Toward climate change refugia conservation at an ecoregion scale. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Cathleen Balantic
- Northeast Climate Adaptation Science Center, Department of Environmental Conservation University of Massachusetts Amherst Amherst Massachusetts USA
| | - Andrea Adams
- Earth Research Institute University of California Santa Barbara Santa Barbara California USA
| | - Shana Gross
- Ecology Program USDA Forest Service, Region 5 South Lake Tahoe California USA
| | - Rachel Mazur
- Division of Resources Management and Science Yosemite National Park El Portal California USA
| | - Sarah Sawyer
- USDA Forest Service, Pacific Southwest Region Vallejo California USA
| | - Jody Tucker
- USDA Forest Service, Pacific Southwest Region Vallejo California USA
| | - Marian Vernon
- Point Blue Conservation Science Petaluma California USA
| | - Claudia Mengelt
- U.S. Fish and Wildlife Service Science Applications Sacramento California USA
| | - Jennifer Morales
- Climate Change Program California Department of Water Resources Fresno California USA
| | - James H. Thorne
- Department of Environmental Science and Policy University of California Davis California USA
| | - Timothy M. Brown
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California USA
| | - Nicole Athearn
- Division of Resources Management and Science National Park Service El Portal California USA
| | - Toni Lyn Morelli
- U.S. Geological Survey, Northeast Climate Adaptation Science Center, Department of Environmental Conservation University of Massachusetts Amherst Amherst Massachusetts USA
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Abstract
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
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Deb JC, Forbes G, MacLean DA. Modelling the spatial distribution of selected North American woodland mammals under future climate scenarios. Mamm Rev 2020. [DOI: 10.1111/mam.12210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jiban Chandra Deb
- Faculty of Forestry and Environmental Management University of New Brunswick Fredericton NBE3B5A3Canada
| | - Graham Forbes
- Faculty of Forestry and Environmental Management University of New Brunswick Fredericton NBE3B5A3Canada
| | - David A. MacLean
- Faculty of Forestry and Environmental Management University of New Brunswick Fredericton NBE3B5A3Canada
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Gremer JR, Chiono A, Suglia E, Bontrager M, Okafor L, Schmitt J. Variation in the seasonal germination niche across an elevational gradient: the role of germination cueing in current and future climates. AMERICAN JOURNAL OF BOTANY 2020; 107:350-363. [PMID: 32056208 DOI: 10.1002/ajb2.1425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/07/2019] [Indexed: 05/22/2023]
Abstract
PREMISE The timing of germination has profound impacts on fitness, population dynamics, and species ranges. Many plants have evolved responses to seasonal environmental cues to time germination with favorable conditions; these responses interact with temporal variation in local climate to drive the seasonal climate niche and may reflect local adaptation. Here, we examined germination responses to temperature cues in Streptanthus tortuosus populations across an elevational gradient. METHODS Using common garden experiments, we evaluated differences among populations in response to cold stratification (chilling) and germination temperature and related them to observed germination phenology in the field. We then explored how these responses relate to past climate at each site and the implications of those patterns under future climate change. RESULTS Populations from high elevations had stronger stratification requirements for germination and narrower temperature ranges for germination without stratification. Differences in germination responses corresponded with elevation and variability in seasonal temperature and precipitation across populations. Further, they corresponded with germination phenology in the field; low-elevation populations germinated in the fall without chilling, whereas high-elevation populations germinated after winter chilling and snowmelt in spring and summer. Climate-change forecasts indicate increasing temperatures and decreasing snowpack, which will likely alter germination cues and timing, particularly for high-elevation populations. CONCLUSIONS The seasonal germination niche for S. tortuosus is highly influenced by temperature and varies across the elevational gradient. Climate change will likely affect germination timing, which may cascade to influence trait expression, fitness, and population persistence.
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Affiliation(s)
- Jennifer R Gremer
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California-Davis, Davis, CA, USA
| | - Alec Chiono
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, 95616, USA
- Department of Biology, University of San Francisco, 2310 Fulton Street, San Francisco, CA, 94117, USA
| | - Elena Suglia
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, 95616, USA
- Population Biology Graduate Group, University of California-Davis, Davis, CA, 95616, USA
| | - Megan Bontrager
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California-Davis, Davis, CA, USA
| | - Lauren Okafor
- Department of Biology, Howard University, 415 College St. NW, Washington, D.C., 20059, USA
| | - Johanna Schmitt
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California-Davis, Davis, CA, USA
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Landscape Connectivity Planning for Adaptation to Future Climate and Land-Use Change. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40823-019-0035-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Morelli TL, Maher SP, Lim MCW, Kastely C, Eastman LM, Flint LE, Flint AL, Beissinger SR, Moritz C. Climate change refugia and habitat connectivity promote species persistence. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s40665-017-0036-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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