1
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Cocciardi JM, Hoffman AM, Alvarado-Serrano DF, Anderson J, Blumstein M, Boehm EL, Bolin LG, Borokini IT, Bradburd GS, Branch HA, Brudvig LA, Chen Y, Collins SL, Des Marais DL, Gamba D, Hanan NP, Howard MM, Jaros J, Juenger TE, Kooyers NJ, Kottler EJ, Lau JA, Menon M, Moeller DA, Mozdzer TJ, Sheth SN, Smith M, Toll K, Ungerer MC, Vahsen ML, Wadgymar SM, Waananen A, Whitney KD, Avolio ML. The value of long-term ecological research for evolutionary insights. Nat Ecol Evol 2024:10.1038/s41559-024-02464-y. [PMID: 39095611 DOI: 10.1038/s41559-024-02464-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/11/2024] [Indexed: 08/04/2024]
Abstract
Scientists must have an integrative understanding of ecology and evolution across spatial and temporal scales to predict how species will respond to global change. Although comprehensively investigating these processes in nature is challenging, the infrastructure and data from long-term ecological research networks can support cross-disciplinary investigations. We propose using these networks to advance our understanding of fundamental evolutionary processes and responses to global change. For ecologists, we outline how long-term ecological experiments can be expanded for evolutionary inquiry, and for evolutionary biologists, we illustrate how observed long-term ecological patterns may motivate new evolutionary questions. We advocate for collaborative, multi-site investigations and discuss barriers to conducting evolutionary work at network sites. Ultimately, these networks offer valuable information and opportunities to improve predictions of species' responses to global change.
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Affiliation(s)
- Jennifer M Cocciardi
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biology, University of Mississippi, Oxford, MS, USA.
| | - Ava M Hoffman
- Department of Biostatistics, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Jill Anderson
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Meghan Blumstein
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emma L Boehm
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Lana G Bolin
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Gideon S Bradburd
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haley A Branch
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lars A Brudvig
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Yanni Chen
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Scott L Collins
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Niall P Hanan
- Department of Plant and Environmental Sciences, Jornada Basin LTER Program, New Mexico State University, Las Cruces, NM, USA
| | - Mia M Howard
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Joseph Jaros
- Department of Biological Sciences, Fordham University, New York, NY, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Nicholas J Kooyers
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Ezra J Kottler
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Jennifer A Lau
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
| | | | - Seema N Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Melinda Smith
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Katherine Toll
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Mark C Ungerer
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Megan L Vahsen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Amy Waananen
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Meghan L Avolio
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA.
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2
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Lott MJ, Frankham GJ, Eldridge MDB, Alquezar‐Planas DE, Donnelly L, Zenger KR, Leigh KA, Kjeldsen SR, Field MA, Lemon J, Lunney D, Crowther MS, Krockenberger MB, Fisher M, Neaves LE. Reversing the decline of threatened koala ( Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 2024; 14:e11700. [PMID: 39091325 PMCID: PMC11289790 DOI: 10.1002/ece3.11700] [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: 02/05/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.
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Affiliation(s)
- Matthew J. Lott
- Australian Museum Research InstituteSydneyNew South WalesAustralia
| | | | | | | | - Lily Donnelly
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kellie A. Leigh
- Science for Wildlife LtdMount VictoriaNew South WalesAustralia
| | - Shannon R. Kjeldsen
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
- Immunogenomics LabGarvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - John Lemon
- JML Environmental ConsultantsArmidaleNew South WalesAustralia
- School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNew South WalesAustralia
| | - Daniel Lunney
- Australian Museum Research InstituteSydneyNew South WalesAustralia
- Department of Planning and EnvironmentParramattaNew South WalesAustralia
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mathew S. Crowther
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark B. Krockenberger
- Sydney School of Veterinary ScienceUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark Fisher
- 3D Ecology MappingEmerald BeachNew South WalesAustralia
| | - Linda E. Neaves
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
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3
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Izaguirre-Toriz V, Aguirre-Liguori JA, Latorre-Cárdenas MC, Arima EY, González-Rodríguez A. Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán. Mol Ecol 2024; 33:e17424. [PMID: 38813851 DOI: 10.1111/mec.17424] [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: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
Climate change and land use change are two main drivers of global biodiversity decline, decreasing the genetic diversity that populations harbour and altering patterns of local adaptation. Landscape genomics allows measuring the effect of these anthropogenic disturbances on the adaptation of populations. However, both factors have rarely been considered simultaneously. Based on a set of 3660 SNPs from which 130 were identified as outliers by a genome-environment association analysis (LFMM), we modelled the spatial turnover of allele frequencies in 19 localities of Pinus leiophylla across the Avocado Belt in Michoacán state, Mexico. Then, we evaluated the effect of climate change and land use change scenarios, in addition to evaluating assisted gene flow strategies and connectivity metrics across the landscape to identify priority conservation areas for the species. We found that localities in the centre-east of the Avocado Belt would be more vulnerable to climate change, while localities in the western area are more threatened by land conversion to avocado orchards. Assisted gene flow actions could aid in mitigating both threats. Connectivity patterns among forest patches will also be modified by future habitat loss, with central and eastern parts of the Avocado Belt maintaining the highest connectivity. These results suggest that areas with the highest priority for conservation are in the eastern part of the Avocado Belt, including the Monarch Butterfly Biosphere Reserve. This work is useful as a framework that incorporates distinct layers of information to provide a more robust representation of the response of tree populations to anthropogenic disturbances.
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Affiliation(s)
- Vanessa Izaguirre-Toriz
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria), Coyoacán, Mexico
| | - Jonás A Aguirre-Liguori
- Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - María Camila Latorre-Cárdenas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Eugenio Y Arima
- Department of Geography and the Environment, University of Texas at Austin, Austin, Texas, USA
| | - Antonio González-Rodríguez
- Laboratorio Nacional de Innovación Ecotecnológica Para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM Campus Morelia, Morelia, Mexico
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4
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Erlichman A, Sandell L, Otto SP, Aitken SN, Ronce O. Planting long-lived trees in a warming climate: Theory shows the importance of stage-dependent climatic tolerance. Evol Appl 2024; 17:e13711. [PMID: 38894979 PMCID: PMC11183180 DOI: 10.1111/eva.13711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 06/21/2024] Open
Abstract
Climate change poses a particular threat to long-lived trees, which may not adapt or migrate fast enough to keep up with rising temperatures. Assisted gene flow could facilitate adaptation of populations to future climates by using managed translocation of seeds from a warmer location (provenance) within the current range of a species. Finding the provenance that will perform best in terms of survival or growth is complicated by a trade-off. Because trees face a rapidly changing climate during their long lives, the alleles that confer optimal performance may vary across their lifespan. For instance, trees from warmer provenances could be well adapted as adults but suffer from colder temperatures while juvenile. Here we use a stage-structured model, using both analytical predictions and numerical simulations, to determine which provenance would maximize the survival of a cohort of long-lived trees in a changing climate. We parameterize our simulations using empirically estimated demographic transition matrices for 20 long-lived tree species. Unable to find reliable quantitative estimates of how climatic tolerance changes across stages in these same species, we varied this parameter to study its effect. Both our mathematical model and simulations predict that the best provenance depends strongly on how fast the climate changes and also how climatic tolerance varies across the lifespan of a tree. We thus call for increased empirical efforts to measure how climate tolerance changes over life in long-lived species, as our model suggests that it should strongly influence the best provenance for assisted gene flow.
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Affiliation(s)
- Adèle Erlichman
- ISEM, Univ Montpellier, CNRS, IRDMontpellierFrance
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Linnea Sandell
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of Organismal BiologyUppsala UniversityUppsalaSweden
- Department of Urban and Rural DevelopmentSwedish University of AgricultureUppsalaSweden
| | - Sarah P. Otto
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Sally N. Aitken
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Ophélie Ronce
- ISEM, Univ Montpellier, CNRS, IRDMontpellierFrance
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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5
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Chen B, Wang M, Guo Y, Zhang Z, Zhou W, Cao L, Zhang T, Ali S, Xie L, Li Y, Zinta G, Sun S, Zhang Q. Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana. Mol Ecol 2024:e17356. [PMID: 38634782 DOI: 10.1111/mec.17356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.
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Affiliation(s)
- Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou, China
| | - Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yile Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zihui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shahid Ali
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Linan Xie
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuhua Li
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shanwen Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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6
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Candido-Ribeiro R, Aitken SN. Weak local adaptation to drought in seedlings of a widespread conifer. THE NEW PHYTOLOGIST 2024; 241:2395-2409. [PMID: 38247230 DOI: 10.1111/nph.19543] [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: 11/20/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well-characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests. We used a large-scale common garden drought-to-death experiment to assess range-wide variation in drought tolerance, measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (Pseudotsuga menziesii var. menziesii and var. glauca). Local adaptation to drought was weak in var. glauca and nearly absent in menziesii. Var. glauca showed higher tolerance to drought but slower growth than var. menziesii. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. menziesii in response to extreme drought. Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.
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Affiliation(s)
- Rafael Candido-Ribeiro
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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7
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Jordan R, Harrison PA, Breed M. The eco-evolutionary risks of not changing seed provenancing practices in changing environments. Ecol Lett 2024; 27:e14348. [PMID: 38288869 DOI: 10.1111/ele.14348] [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: 06/01/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 02/01/2024]
Abstract
Sourcing seed from local populations has been the long-standing default for native restoration plantings for numerous eco-evolutionary reasons. However, rapidly changing environments are revealing risks associated with both non-local and local provenancing. As alternative strategies gain interest, we argue to progress seed sourcing discussions towards developing risk-based decision-making that weighs the risks of changing and not changing in a changing environment, transcending historic default positions and local versus non-local debates.
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Affiliation(s)
| | - Peter A Harrison
- Australian Research Council Centre for Forest Value & School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Martin Breed
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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Hoste A, Capblancq T, Broquet T, Denoyelle L, Perrier C, Buzan E, Šprem N, Corlatti L, Crestanello B, Hauffe HC, Pellissier L, Yannic G. Projection of current and future distribution of adaptive genetic units in an alpine ungulate. Heredity (Edinb) 2024; 132:54-66. [PMID: 38082151 PMCID: PMC10798982 DOI: 10.1038/s41437-023-00661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/21/2024] Open
Abstract
Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.
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Affiliation(s)
- Amélie Hoste
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Thibaut Capblancq
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Thomas Broquet
- CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Charles Perrier
- UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000, Zagreb, Croatia
| | - Luca Corlatti
- Stelvio National Park - ERSAF Lombardia, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Barbara Crestanello
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Loïc Pellissier
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zrich, Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Glenn Yannic
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
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9
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Maroso F, Padovani G, Muñoz Mora VH, Giannelli F, Trucchi E, Bertorelle G. Fitness consequences and ancestry loss in the Apennine brown bear after a simulated genetic rescue intervention. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14133. [PMID: 37259604 DOI: 10.1111/cobi.14133] [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: 07/05/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 06/02/2023]
Abstract
Reduction in population size, with its predicted effects on population fitness, is the most alarming anthropogenic impact on endangered species. By introducing compatible individuals, genetic rescue (GR) is a promising but debated approach for reducing the genetic load unmasked by inbreeding and for restoring the fitness of declining populations. Although GR can improve genetic diversity and fitness, it can also produce loss of ancestry, hampering local adaptation, or replace with introduced variants the unique genetic pools evolved in endemic groups. We used forward genetic simulations based on empirical genomic data to assess fitness benefits and loss of ancestry risks of GR in the Apennine brown bear (Ursus arctos marsicanus). There are approximately 50 individuals of this isolated subspecies, and they have lower genetic diversity and higher inbreeding than other European brown bears, and GR has been suggested to reduce extinction risks. We compared 10 GR scenarios in which the number and genetic characteristics of migrants varied with a non-GR scenario of simple demographic increase due to nongenetic factors. The introduction of 5 individuals of higher fitness or lower levels of deleterious mutations than the target Apennine brown bear from a larger European brown bear population produced a rapid 10-20% increase in fitness in the subspecies and up to 22.4% loss of ancestry over 30 generations. Without a contemporary demographic increase, fitness started to decline again after a few generations. Doubling the population size without GR gradually increased fitness to a comparable level, but without losing ancestry, thus resulting in the best strategy for the Apennine brown bear conservation. Our results highlight the importance for management of endangered species of realistic forward simulations grounded in empirical whole-genome data.
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Affiliation(s)
- Francesco Maroso
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Giada Padovani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Francesco Giannelli
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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10
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Feng S, Xi E, Wan W, Ru D. Genomic signals of local adaptation in Picea crassifolia. BMC PLANT BIOLOGY 2023; 23:534. [PMID: 37919677 PMCID: PMC10623705 DOI: 10.1186/s12870-023-04539-7] [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: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. RESULTS Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. CONCLUSIONS Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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11
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Chambers EA, Bishop AP, Wang IJ. Individual-based landscape genomics for conservation: An analysis pipeline. Mol Ecol Resour 2023. [PMID: 37883295 DOI: 10.1111/1755-0998.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/18/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
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Affiliation(s)
- E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
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12
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Leites L, Benito Garzón M. Forest tree species adaptation to climate across biomes: Building on the legacy of ecological genetics to anticipate responses to climate change. GLOBAL CHANGE BIOLOGY 2023; 29:4711-4730. [PMID: 37029765 DOI: 10.1111/gcb.16711] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Intraspecific variation plays a critical role in extant and future forest responses to climate change. Forest tree species with wide climatic niches rely on the intraspecific variation resulting from genetic adaptation and phenotypic plasticity to accommodate spatial and temporal climate variability. A centuries-old legacy of forest ecological genetics and provenance trials has provided a strong foundation upon which to continue building on this knowledge, which is critical to maintain climate-adapted forests. Our overall objective is to understand forest trees intraspecific responses to climate across species and biomes, while our specific objectives are to describe ecological genetics models used to build our foundational knowledge, summarize modeling approaches that have expanded the traditional toolset, and extensively review the literature from 1994 to 2021 to highlight the main contributions of this legacy and the new analyzes of provenance trials. We reviewed 103 studies comprising at least three common gardens, which covered 58 forest tree species, 28 of them with range-wide studies. Although studies using provenance trial data cover mostly commercially important forest tree species from temperate and boreal biomes, this synthesis provides a global overview of forest tree species adaptation to climate. We found that evidence for genetic adaptation to local climate is commonly present in the species studied (79%), being more common in conifers (87.5%) than in broadleaf species (67%). In 57% of the species, clines in fitness-related traits were associated with temperature variables, in 14% of the species with precipitation, and in 25% of the species with both. Evidence of adaptation lags was found in 50% of the species with range-wide studies. We conclude that ecological genetics models and analysis of provenance trial data provide excellent insights on intraspecific genetic variation, whereas the role and limits of phenotypic plasticity, which will likely determine the fate of extant forests, is vastly understudied.
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Affiliation(s)
- Laura Leites
- Department of Ecosystem Science and Management, Penn State University, University Park, Pennsylvania, USA
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13
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Méndez-Cea B, García-García I, Linares JC, Gallego FJ. Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios. FRONTIERS IN PLANT SCIENCE 2023; 14:1155441. [PMID: 37636100 PMCID: PMC10451094 DOI: 10.3389/fpls.2023.1155441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023]
Abstract
Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.
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Affiliation(s)
- Belén Méndez-Cea
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel García-García
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Dpto. Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Francisco Javier Gallego
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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14
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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15
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Capblancq T, Lachmuth S, Fitzpatrick MC, Keller SR. From common gardens to candidate genes: exploring local adaptation to climate in red spruce. THE NEW PHYTOLOGIST 2023; 237:1590-1605. [PMID: 36068997 PMCID: PMC10092705 DOI: 10.1111/nph.18465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/09/2022] [Indexed: 05/12/2023]
Abstract
Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two 'modules' associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant BiologyUniversity of VermontBurlingtonVT05405USA
| | - Susanne Lachmuth
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMD21532USA
| | - Matthew C. Fitzpatrick
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMD21532USA
| | - Stephen R. Keller
- Department of Plant BiologyUniversity of VermontBurlingtonVT05405USA
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16
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Palumbi SR, Walker NS, Hanson E, Armstrong K, Lippert M, Cornwell B, Nestor V, Golbuu Y. Small-scale genetic structure of coral populations in Palau based on whole mitochondrial genomes: Implications for future coral resilience. Evol Appl 2023; 16:518-529. [PMID: 36793699 PMCID: PMC9923468 DOI: 10.1111/eva.13509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 01/07/2023] Open
Abstract
The ability of local populations to adapt to future climate conditions is facilitated by a balance between short range dispersal allowing local buildup of adaptively beneficial alleles, and longer dispersal moving these alleles throughout the species range. Reef building corals have relatively low dispersal larvae, but most population genetic studies show differentiation only over 100s of km. Here, we report full mitochondrial genome sequences from 284 tabletop corals (Acropora hyacinthus) from 39 patch reefs in Palau, and show two signals of genetic structure across reef scales from 1 to 55 km. First, divergent mitochondrial DNA haplotypes exist in different proportions from reef to reef, causing PhiST values of 0.02 (p = 0.02). Second, closely related sequences of mitochondrial Haplogroups are more likely to be co-located on the same reefs than expected by chance alone. We also compared these sequences to prior data on 155 colonies from American Samoa. In these comparisons, many Haplogroups in Palau were disproportionately represented or absent in American Samoa, and inter-regional PhiST = 0.259. However, we saw three instances of identical mitochondrial genomes between locations. Together, these data sets suggest two features of coral dispersal revealed by occurrence patterns in highly similar mitochondrial genomes. First, the Palau-American Samoa data suggest that long distance dispersal in corals is rare, as expected, but that it is common enough to deliver identical mitochondrial genomes across the Pacific. Second, higher than expected co-occurrence of Haplogroups on the same Palau reefs suggests greater retention of coral larvae on local reefs than predicted by many current oceanographic models of larval movement. Increased attention to local scales of coral genetic structure, dispersal, and selection may help increase the accuracy of models of future adaptation of corals and of assisted migration as a reef resilience intervention.
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Affiliation(s)
- Stephen R Palumbi
- Department of Biology and Oceans Department Hopkins Marine Station of Stanford University Pacific Grove California USA
| | - Nia S Walker
- Department of Biology and Oceans Department Hopkins Marine Station of Stanford University Pacific Grove California USA.,Hawaii Institute of Marine Biology, University of Hawaii Honolulu Hawaii USA
| | - Erik Hanson
- Department of Biology and Oceans Department Hopkins Marine Station of Stanford University Pacific Grove California USA
| | - Katrina Armstrong
- Department of Biology and Oceans Department Hopkins Marine Station of Stanford University Pacific Grove California USA
| | - Marilla Lippert
- Department of Biology and Oceans Department Hopkins Marine Station of Stanford University Pacific Grove California USA
| | - Brendan Cornwell
- Department of Biology and Oceans Department Hopkins Marine Station of Stanford University Pacific Grove California USA
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17
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Nocchi G, Wang J, Yang L, Ding J, Gao Y, Buggs RJA, Wang N. Genomic signals of local adaptation and hybridization in Asian white birch. Mol Ecol 2023; 32:595-612. [PMID: 36394364 DOI: 10.1111/mec.16788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Disentangling the numerous processes that affect patterns of genome-wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing data set for 79 European and Russian white birches, we show a clear distinction between B. pendula and B. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity of B. platyphylla in north-western China and Central Russia is affected greatly by hybridization with B. pendula. Excluding these hybridized populations, B. platyphylla in China has a linear distribution from north-eastern to south-western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of covariation between allele frequencies and environmental variables in B. platyphylla suggest the role of natural selection in the distribution of diversity at 7609 SNPs of which 3767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in Eurasian B. pendula. We use the 7609 environmentally associated SNPs to estimate the risk of nonadaptedness for each sequenced B. platyphylla individual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.
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Affiliation(s)
- Gabriele Nocchi
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Jing Wang
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Long Yang
- Agricultural Big-Data Research Centre and College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Junyi Ding
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Ying Gao
- Agricultural Big-Data Research Centre and College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Richard J A Buggs
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Nian Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
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18
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Yuan S, Shi Y, Zhou BF, Liang YY, Chen XY, An QQ, Fan YR, Shen Z, Ingvarsson PK, Wang B. Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests. Mol Ecol 2023; 32:1639-1655. [PMID: 36626136 DOI: 10.1111/mec.16843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima, in East Asia, and applied genome-wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype-environment association analyses, we identified climate-associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima. We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene-environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome-wide view of climate maladaptation in Q. acutissima.
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Affiliation(s)
- Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Yan-Ru Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Zhao Shen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou, China.,South China National Botanical Garden, Guangzhou, China
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19
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Wang Y, Zhang L, Zhou Y, Ma W, Li M, Guo P, Feng L, Fu C. Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China. Front Genet 2023; 14:1150704. [PMID: 37144128 PMCID: PMC10151583 DOI: 10.3389/fgene.2023.1150704] [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: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.
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Affiliation(s)
- Yihan Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Lin Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Yuchao Zhou
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Wenxin Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Manyu Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Peng Guo
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
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20
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Meek MH, Beever EA, Barbosa S, Fitzpatrick SW, Fletcher NK, Mittan-Moreau CS, Reid BN, Campbell-Staton SC, Green NF, Hellmann JJ. Understanding Local Adaptation to Prepare Populations for Climate Change. Bioscience 2022. [DOI: 10.1093/biosci/biac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.
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Affiliation(s)
- Mariah H Meek
- Department of Integrative Biology, AgBio Research, and the Ecology, Evolution, and Behavior Program Michigan State University , East Lansing, Michigan, United States
| | - Erik A Beever
- Department of Ecology, Montana State University , Bozeman, Montana, United States
| | - Soraia Barbosa
- Department of Fish and Wildlife Sciences, University of Idaho , Moscow, Idaho, United States
| | - Sarah W Fitzpatrick
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
| | - Nicholas K Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
- Department of Biology, University of Maryland , College Park, Maryland, United States
| | - Cinnamon S Mittan-Moreau
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
| | - Brendan N Reid
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology, Evolution, and Natural Resources, Rutgers University , New Brunswick, New Jersey, United States
| | - Shane C Campbell-Staton
- Department of Ecology and Evolutionary Biology, Princeton University , Princeton, New Jersey, United States
| | - Nancy F Green
- US Fish and Wildlife Service, Falls Church , Virginia, United States
| | - Jessica J Hellmann
- Institute of the Environment and Department of Ecology, Evolution, and Behavior, University of Minnesota , Saint Paul, Minnesota, United States
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21
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Shaffer HB, Toffelmier E, Corbett-Detig RB, Escalona M, Erickson B, Fiedler P, Gold M, Harrigan RJ, Hodges S, Luckau TK, Miller C, Oliveira DR, Shaffer KE, Shapiro B, Sork VL, Wang IJ. Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project. J Hered 2022; 113:577-588. [PMID: 35395669 DOI: 10.1093/jhered/esac020] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 12/16/2022] Open
Abstract
The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Russ B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bjorn Erickson
- U.S. Fish and Wildlife Service, Sacramento, CA 95825, USA
| | - Peggy Fiedler
- Natural Reserve System, Office of the President, University of California, Oakland, CA 94607, USA
| | - Mark Gold
- California Natural Resources Agency, 1416 Ninth Street, Suite 1311, Sacramento, CA 95814, USA
| | - Ryan J Harrigan
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Center for Tropical Research, Institute for Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Scott Hodges
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Tara K Luckau
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Daniel R Oliveira
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Kevin E Shaffer
- California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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22
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Hama AA, Khwarahm NR. Predictive mapping of two endemic oak tree species under climate change scenarios in a semiarid region: Range overlap and implications for conservation. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat Commun 2022; 13:6541. [PMID: 36319648 PMCID: PMC9626627 DOI: 10.1038/s41467-022-34206-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.
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24
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Ding C, Brouard JS. Assisted migration is plausible for a boreal tree species under climate change: A quantitative and population genetics study of trembling aspen ( Populus tremuloides Michx.) in western Canada. Ecol Evol 2022; 12:e9384. [PMID: 36225831 PMCID: PMC9534759 DOI: 10.1002/ece3.9384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/16/2022] [Indexed: 11/14/2022] Open
Abstract
A novel method was tested for improving tree breeding strategies that integrate quantitative and population genetics based on range‐wide reciprocal transplant experiments. Five reciprocal common garden tests of Populus tremuloides were investigated including 6450 trees across western Canada focusing on adaptation traits and growth. Both genetic parameters and home‐site transplant models were evaluated. We found a genetic trade‐off between growth and early spring leaf flush and late fall senescence. Coefficients of phenotypic variation (CVp) of cell lysis (CL), a measure of freezing injury, shrank from 0.28 to 0.10 during acclimation in the fall, and the CVp slope versus the freezing temperature was significantly different from zero (R2 = 0.33, p = .02). There was more between‐population genetic variation in fall phenology than in spring leaf phenology. We suggest that P. tremuloides demonstrated a discrepancy between the ecological optimum and the physiological optimum minimum winter temperature. The sub‐optimal growing condition of P. tremuloides is potentially caused by the warmer ecological optimum than the physiological optimum. Assisted migration and breeding of fast growers to reforest cooler plantation sites can improve productivity. Transferring the study populations to less than 4°C of extreme minimum temperature appears safe for reforestation aligning with the historical recolonization direction of the species. This is equivalent to a 5–10° latitudinal northward movement. Fall frost hardiness is an effective criterion for family selection in the range tested in this study.
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Affiliation(s)
- Chen Ding
- Western Gulf Forest Tree Improvement ProgramTexas A&M Forest Service, TAMU SystemCollege StationTexasUSA
| | - Jean S. Brouard
- Isabella Point Forestry Ltd.Salt Spring IslandBritish ColumbiaCanada
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25
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Liu Y, Erbilgin N, Ratcliffe B, Klutsch JG, Wei X, Ullah A, Cappa EP, Chen C, Thomas BR, El-Kassaby YA. Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations. Proc Biol Sci 2022; 289:20221034. [PMID: 36069017 PMCID: PMC9449467 DOI: 10.1098/rspb.2022.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
While droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e. height growth, drought avoidance based on water-use efficiency inferred from δ13C and pest resistance based on defence traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ13C and increased the evolutionary potential of height growth and δ13C across populations. We found, however, no pronounced gradient in defences and their evolutionary potential along populations or test sites. Response to selection was weak in defences across test sites, but high for height growth particularly at warm test sites. Response to the selection of δ13C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with a limited evolutionary influence from pest (biotic) pressures.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada.,McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK.,Wolfson College, University of Cambridge, Barton Road, Cambridge CB3 9BB, UK
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jennifer G Klutsch
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Xiaojing Wei
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Aziz Ullah
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Eduardo Pablo Cappa
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Recursos Biológicos, Centro de Investigación en Recursos Naturales, De Los Reseros y Doctor Nicolás Repetto s/n, 1686, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Barb R Thomas
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
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26
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DeSaix MG, George TL, Seglund AE, Spellman GM, Zavaleta ES, Ruegg KC. Forecasting climate change response in an alpine specialist songbird reveals the importance of considering novel climate. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Matthew G. DeSaix
- Department of Biology Colorado State University Fort Collins Colorado USA
| | - T. Luke George
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado USA
| | | | - Garth M. Spellman
- Department of Zoology Denver Museum of Nature and Science Denver Colorado USA
| | - Erika S. Zavaleta
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins Colorado USA
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27
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Cooper HF, Best RJ, Andrews LV, Corbin JPM, Garthwaite I, Grady KC, Gehring CA, Hultine KR, Whitham TG, Allan GJ. Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species. Mol Ecol 2022; 31:5024-5040. [PMID: 35947510 DOI: 10.1111/mec.16645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST -FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST -FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.
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Affiliation(s)
- Hillary F Cooper
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca J Best
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Lela V Andrews
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Jaclyn P M Corbin
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Iris Garthwaite
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin C Grady
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Catherine A Gehring
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, USA
| | - Thomas G Whitham
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Gerard J Allan
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
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28
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Bonnet T, Morrissey MB, de Villemereuil P, Alberts SC, Arcese P, Bailey LD, Boutin S, Brekke P, Brent LJN, Camenisch G, Charmantier A, Clutton-Brock TH, Cockburn A, Coltman DW, Courtiol A, Davidian E, Evans SR, Ewen JG, Festa-Bianchet M, de Franceschi C, Gustafsson L, Höner OP, Houslay TM, Keller LF, Manser M, McAdam AG, McLean E, Nietlisbach P, Osmond HL, Pemberton JM, Postma E, Reid JM, Rutschmann A, Santure AW, Sheldon BC, Slate J, Teplitsky C, Visser ME, Wachter B, Kruuk LEB. Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals. Science 2022; 376:1012-1016. [PMID: 35617403 DOI: 10.1126/science.abk0853] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.
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Affiliation(s)
- Timothée Bonnet
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études, PSL, MNHN, CNRS, SU, UA, Paris, France.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan C Alberts
- Departments of Biology and Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Peter Arcese
- Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam D Bailey
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Penryn, UK
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Tim H Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, UK.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew Cockburn
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Alexandre Courtiol
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Eve Davidian
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simon R Evans
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | | | - Christophe de Franceschi
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lars Gustafsson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Oliver P Höner
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Thomas M Houslay
- Department of Zoology, University of Cambridge, Cambridge, UK.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich,, Zurich, Switzerland
| | - Marta Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew G McAdam
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Emily McLean
- Biology Department, Oxford College, Emory University, Oxford, GA, USA
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Helen L Osmond
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Erik Postma
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Jane M Reid
- Centre for Biodiversity Dynamics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alexis Rutschmann
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - Jon Slate
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Céline Teplitsky
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Bettina Wachter
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Loeske E B Kruuk
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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29
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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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Aurelle D, Thomas S, Albert C, Bally M, Bondeau A, Boudouresque C, Cahill AE, Carlotti F, Chenuil A, Cramer W, Davi H, De Jode A, Ereskovsky A, Farnet A, Fernandez C, Gauquelin T, Mirleau P, Monnet A, Prévosto B, Rossi V, Sartoretto S, Van Wambeke F, Fady B. Biodiversity, climate change, and adaptation in the Mediterranean. Ecosphere 2022. [DOI: 10.1002/ecs2.3915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS Sorbonne Université, EPHE Paris France
| | - Séverine Thomas
- Aix Marseille Université, Labex‐OT‐Med Aix‐en‐Provence France
| | - Cécile Albert
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Marc Bally
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Alberte Bondeau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - François Carlotti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Wolfgang Cramer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Hendrik Davi
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
| | - Aurélien De Jode
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Department of Marine Sciences‐Tjärnö University of Gothenburg, Tjärnö Marine Laboratory Gothenburg Sweden
| | - Alexander Ereskovsky
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Saint‐Petersburg State University St. Petersburg Russia
| | - Anne‐Marie Farnet
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | - Thierry Gauquelin
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Pascal Mirleau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - Vincent Rossi
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | | | - France Van Wambeke
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Bruno Fady
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
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31
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Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nat Commun 2022; 13:2047. [PMID: 35440538 PMCID: PMC9018854 DOI: 10.1038/s41467-022-29584-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA.
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Shawn J Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jesse A Garcia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Steven L Salzberg
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA
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32
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Thurman LL, Gross JE, Mengelt C, Beever EA, Thompson LM, Schuurman GW, Hoving CL, Olden JD. Applying assessments of adaptive capacity to inform natural-resource management in a changing climate. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13838. [PMID: 34622995 DOI: 10.1111/cobi.13838] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Adaptive capacity (AC)-the ability of a species to cope with or accommodate climate change-is a critical determinant of species vulnerability. Using information on species' AC in conservation planning is key to ensuring successful outcomes. We identified connections between a list of species' attributes (e.g., traits, population metrics, and behaviors) that were recently proposed for assessing species' AC and management actions that may enhance AC for species at risk of extinction. Management actions were identified based on evidence from the literature, a review of actions used in other climate adaptation guidance, and our collective experience in diverse fields of global-change ecology and climate adaptation. Selected management actions support the general AC pathways of persist in place or shift in space, in response to contemporary climate change. Some actions, such as genetic manipulations, can be used to directly alter the ability of species to cope with climate change, whereas other actions can indirectly enhance AC by addressing ecological or anthropogenic constraints on the expression of a species' innate abilities to adapt. Ours is the first synthesis of potential management actions directly linked to AC. Focusing on AC attributes helps improve understanding of how and why aspects of climate are affecting organisms, as well as the mechanisms by which management interventions affect a species' AC and climate change vulnerability. Adaptive-capacity-informed climate adaptation is needed to build connections among the causes of vulnerability, AC, and proposed management actions that can facilitate AC and reduce vulnerability in support of evolving conservation paradigms.
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Affiliation(s)
- Lindsey L Thurman
- U.S. Geological Survey, Northwest Climate Adaptation Science Center, Corvallis, Oregon, USA
| | - John E Gross
- National Park Service, Climate Change Response Program, Fort Collins, Colorado, USA
| | - Claudia Mengelt
- U.S. Geological Survey, Land Management Research Program, Sacramento, California, USA
| | - Erik A Beever
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA
- Department of Ecology, Montana State University, Bozeman, Montana, USA
| | - Laura M Thompson
- U.S. Geological Survey, National Climate Adaptation Science Center, Reston, Virginia, USA
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, Tennessee, USA
| | - Gregor W Schuurman
- National Park Service, Climate Change Response Program, Fort Collins, Colorado, USA
| | | | - Julian D Olden
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
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33
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Lott MJ, Wright BR, Neaves LE, Frankham GJ, Dennison S, Eldridge MDB, Potter S, Alquezar-Planas DE, Hogg CJ, Belov K, Johnson RN. Future-proofing the koala: synergising genomic and environmental data for effective species management. Mol Ecol 2022; 31:3035-3055. [PMID: 35344635 DOI: 10.1111/mec.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
Abstract
Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (∼ 430-300 kya), a major climatic reorganization that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of threatened populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g. guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.
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Affiliation(s)
- Matthew J Lott
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Belinda R Wright
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia.,Sydney School of Veterinary Sciences, Faculty of Science, the University of Sydney, 2006, New South Wales, Australia
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Fenner School of Environment and Society, the Australian National University, Canberra, Australian Capital Territory, 2600, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Sally Potter
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,Division of Ecology & Evolution, Research School of Biology, the Australian National University, Australian Capital Territory, Canberra, 2600, Australia
| | - David E Alquezar-Planas
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, the University of Sydney, 2006, New South Wales, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, 2010, New South Wales, Australia.,National Museum of Natural History, District of Columbia, Washington, 20560, United States
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34
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Bragg JG, van der Merwe M, Yap JYS, Borevitz J, Rossetto M. Plant collections for conservation and restoration: can they be adapted and adaptable? Mol Ecol Resour 2022; 22:2171-2182. [PMID: 35229464 DOI: 10.1111/1755-0998.13605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022]
Abstract
Plant collections are important for the conservation of threatened species, and can provide material for ecological restoration. Typically we want collections to have high genetic diversity so populations founded from it are adaptable to future challenges. Sometimes, we have additional objectives for collections, such as enrichment for desirable traits controlled by adaptive alleles. We used landscape genomic datasets for two plants, Westringia fruticosa and Wilkiea huegeliana, to design collections that are genetically diverse, and that are adapted to warming climates. We characterized temperature adaptation by: (i) using the mean annual temperature of the sites of origin of the plants, and (ii) using the representation of alleles that are associated with warm temperatures. In Westringia fruticosa, there was a negative correlation, or tradeoff, between designing a collection that was both genetically diverse and adapted to warm temperatures. This tradeoff was weaker in Wilkiea huegeliana. We hypothesized this was because neutral genetic variation was strongly correlated with temperature in Westringia fruticosa, and not in Wilkiea huegeliana. Accordingly, when we shuffled the temperature data, breaking up the covariance between Westringia fruticosa genetic variation and temperature, there was a relaxation of the observed tradeoff. In sum, we explore tradeoffs between promoting genetic diversity and selecting for a specific trait in plant collections, and show that the strength of this tradeoff varies between two species. This represents a useful step towards understanding when selection will have a large cost in genetic diversity, and when it will be possible to design a collection that is both adapted and adaptable.
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Affiliation(s)
- Jason G Bragg
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia.,School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
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35
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Moran EV, Thuiller W, Angert AL, Benito Garzón M. Editorial: Predicting and Managing Climate-Driven Range Shifts in Plants. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.856213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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37
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Feng L, Du FK. Landscape Genomics in Tree Conservation Under a Changing Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:822217. [PMID: 35283901 PMCID: PMC8908315 DOI: 10.3389/fpls.2022.822217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/10/2022] [Indexed: 05/11/2023]
Abstract
Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fang K. Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Fang K. Du,
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38
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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39
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Fontes CG, Pinto‐Ledezma J, Jacobsen AL, Pratt RB, Cavender‐Bares J. Adaptive variation among oaks in wood anatomical properties is shaped by climate of origin and shows limited plasticity across environments. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clarissa G. Fontes
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul MN USA
| | - Jesús Pinto‐Ledezma
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul MN USA
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40
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Greenspoon PB, Spencer HG. Avoiding extinction under nonlinear environmental change: models of evolutionary rescue with plasticity. Biol Lett 2021; 17:20210459. [PMID: 34875181 PMCID: PMC8651410 DOI: 10.1098/rsbl.2021.0459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here, we present a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change.
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Affiliation(s)
| | - Hamish G. Spencer
- Department of Zoology, University of Otago, Dunedin 9016, New Zealand
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41
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McLaughlin B, Fogg A, Ennis KK, Halstrom G, Herrera A, Quadri P. Climate change‐adaptive participatory field gene banking for a California endemic oak. Restor Ecol 2021. [DOI: 10.1111/rec.13573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Alissa Fogg
- Point Blue Conservation Science 3820 Cypress Drive #11 Petaluma CA 94954 U.S.A
| | - Katherine K. Ennis
- Department of Integrative Biology University of California, Berkeley Berkeley CA 94720 U.S.A
| | - Grant Halstrom
- Point Blue Conservation Science 3820 Cypress Drive #11 Petaluma CA 94954 U.S.A
| | - Alicia Herrera
- Point Blue Conservation Science 3820 Cypress Drive #11 Petaluma CA 94954 U.S.A
| | - Paulo Quadri
- Sky Island Alliance 3127 N Cherry Avenue Tucson AZ 85719 U.S.A
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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Ramírez-Valiente JA, Solé-Medina A, Pyhäjärvi T, Savolainen O, Heer K, Opgenoorth L, Danusevicius D, Robledo-Arnuncio JJ. Adaptive responses to temperature and precipitation variation at the early-life stages of Pinus sylvestris. THE NEW PHYTOLOGIST 2021; 232:1632-1647. [PMID: 34388269 DOI: 10.1111/nph.17678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Early-stage fitness variation has been seldom evaluated at broad scales in forest tree species, despite the long tradition of studying climate-driven intraspecific genetic variation. In this study, we evaluated the role of climate in driving patterns of population differentiation at early-life stages in Pinus sylvestris and explored the fitness and growth consequences of seed transfer within the species range. We monitored seedling emergence, survival and growth over a 2-yr period in a multi-site common garden experiment which included 18 European populations and spanned 25° in latitude and 1700 m in elevation. Climate-fitness functions showed that populations exhibited higher seedling survival and growth at temperatures similar to their home environment, which is consistent with local adaptation. Northern populations experienced lower survival and growth at warmer sites, contrary to previous studies on later life stages. Seed mass was higher in populations from warmer areas and was positively associated with survival and growth at more southern sites. Finally, we did not detect a survival-growth trade-off; on the contrary, bigger seedlings exhibited higher survival probabilities under most climatic conditions. In conclusion, our results reveal that contrasting temperature regimes have played an important role in driving the divergent evolution of P. sylvestris populations at early-life stages.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
- Ecological and Forestry Applications Research Centre, CREAF, Campus de Bellaterra (UAB) Edifici C 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Aida Solé-Medina
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
- Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, C/Tulipán s/n, Móstoles, 28933, Spain
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, FI-90014, Finland
- Department of Forest Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Outi Savolainen
- Conservation Biology, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Katrin Heer
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Darius Danusevicius
- Faculty of Forest Science and Evology, Vytautas Magnus University, Studentu str. 11, Akademija, Kaunas, LT-53361, Lithuania
| | - Juan José Robledo-Arnuncio
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
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Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer. Proc Natl Acad Sci U S A 2021; 118:2016900118. [PMID: 33649218 PMCID: PMC7958292 DOI: 10.1073/pnas.2016900118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Temperate trees originating from warmer localities usually grow faster and acclimate to winter later than trees of the same species from colder localities. However, when trees are selected for faster growth, are climatically adaptive genes and traits affected? Our research demonstrates a simple, sensitive, broadly applicable, and elusive approach to integrating complex polygenic variation into applied environmental management. We show that selective breeding increases allele frequencies of many trait-associated genes, and that alleles that increase most display strong genetic linkage and potential trade-offs among traits. Increasing tree growth while maintaining adaptation is essential to reforestation in a changing climate, but this may be challenging because trait-associated genetic variation that underpins climate adaptation is responsive to selection for tree growth. Locally adapted temperate tree populations exhibit genetic trade-offs among climate-related traits that can be exacerbated by selective breeding and are challenging to manage under climate change. To inform climatically adaptive forest management, we investigated the genetic architecture and impacts of selective breeding on four climate-related traits in 105 natural and 20 selectively bred lodgepole pine populations from western Canada. Growth, cold injury, growth initiation, and growth cessation phenotypes were tested for associations with 18,600 single-nucleotide polymorphisms (SNPs) in natural populations to identify “positive effect alleles” (PEAs). The effects of artificial selection for faster growth on the frequency of PEAs associated with each trait were quantified in breeding populations from different climates. Substantial shifts in PEA proportions and frequencies were observed across many loci after two generations of selective breeding for height, and responses of phenology-associated PEAs differed strongly among climatic regions. Extensive genetic overlap was evident among traits. Alleles most strongly associated with greater height were often associated with greater cold injury and delayed phenology, although it is unclear whether potential trade-offs arose directly from pleiotropy or indirectly via genetic linkage. Modest variation in multilocus PEA frequencies among populations was associated with large phenotypic differences and strong climatic gradients, providing support for assisted gene flow polices. Relationships among genotypes, phenotypes, and climate in natural populations were maintained or strengthened by selective breeding. However, future adaptive phenotypes and assisted gene flow may be compromised if selective breeding further increases the PEA frequencies of SNPs involved in adaptive trade-offs among climate-related traits.
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Vranken S, Wernberg T, Scheben A, Severn-Ellis AA, Batley J, Bayer PE, Edwards D, Wheeler D, Coleman MA. Genotype-Environment mismatch of kelp forests under climate change. Mol Ecol 2021; 30:3730-3746. [PMID: 34018645 DOI: 10.1111/mec.15993] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/23/2023]
Abstract
Climate change is increasingly impacting ecosystems globally. Understanding adaptive genetic diversity and whether it will keep pace with projected climatic change is necessary to assess species' vulnerability and design efficient mitigation strategies such as assisted adaptation. Kelp forests are the foundations of temperate reefs globally but are declining in many regions due to climate stress. A lack of knowledge of kelp's adaptive genetic diversity hinders assessment of vulnerability under extant and future climates. Using 4245 single nucleotide polymorphisms (SNPs), we characterized patterns of neutral and putative adaptive genetic diversity for the dominant kelp in the southern hemisphere (Ecklonia radiata) from ~1000 km of coastline off Western Australia. Strong population structure and isolation-by-distance was underpinned by significant signatures of selection related to temperature and light. Gradient forest analysis of temperature-linked SNPs under selection revealed a strong association with mean annual temperature range, suggesting adaptation to local thermal environments. Critically, modelling revealed that predicted climate-mediated temperature changes will probably result in high genomic vulnerability via a mismatch between current and future predicted genotype-environment relationships such that kelp forests off Western Australia will need to significantly adapt to keep pace with projected climate change. Proactive management techniques such as assisted adaptation to boost resilience may be required to secure the future of these kelp forests and the immense ecological and economic values they support.
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Affiliation(s)
- Sofie Vranken
- UWA Oceans Institute, Crawley, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Thomas Wernberg
- UWA Oceans Institute, Crawley, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Institute of Marine Research, His, Norway
| | - Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Philipp Emanuel Bayer
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - David Wheeler
- New South Wales Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia
| | - Melinda Ann Coleman
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- New South Wales Fisheries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
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Abstract
Quercus species (oaks) have been an integral part of the landscape in the northern hemisphere for millions of years. Their ability to adapt and spread across different environments and their contributions to many ecosystem services is well documented. Human activity has placed many oak species in peril by eliminating or adversely modifying habitats through exploitative land usage and by practices that have exacerbated climate change. The goal of this review is to compile a list of oak species of conservation concern, evaluate the genetic data that is available for these species, and to highlight the gaps that exist. We compiled a list of 124 Oaks of Concern based on the Red List of Oaks 2020 and the Conservation Gap Analysis for Native U.S. Oaks and their evaluations of each species. Of these, 57% have been the subject of some genetic analysis, but for most threatened species (72%), the only genetic analysis was done as part of a phylogenetic study. While nearly half (49%) of published genetic studies involved population genetic analysis, only 16 species of concern (13%) have been the subject of these studies. This is a critical gap considering that analysis of intraspecific genetic variability and genetic structure are essential for designing conservation management strategies. We review the published population genetic studies to highlight their application to conservation. Finally, we discuss future directions in Quercus conservation genetics and genomics.
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Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [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: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
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Rellstab C, Dauphin B, Exposito‐Alonso M. Prospects and limitations of genomic offset in conservation management. Evol Appl 2021; 14:1202-1212. [PMID: 34025760 PMCID: PMC8127717 DOI: 10.1111/eva.13205] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
In nature conservation, there is keen interest in predicting how populations will respond to environmental changes such as climate change. These predictions can help determine whether a population can be self-sustaining under future alterations of its habitat or whether it may require human intervention such as protection, restoration, or assisted migration. An increasingly popular approach in this respect is the concept of genomic offset, which combines genomic and environmental data from different time points and/or locations to assess the degree of possible maladaptation to new environmental conditions. Here, we argue that the concept of genomic offset holds great potential, but an exploration of its risks and limitations is needed to use it for recommendations in conservation or assisted migration. After briefly describing the concept, we list important issues to consider (e.g., statistical frameworks, population genetic structure, migration, independent evidence) when using genomic offset or developing these methods further. We conclude that genomic offset is an area of development that still lacks some important features and should be used in combination with other approaches to inform conservation measures.
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Affiliation(s)
| | | | - Moises Exposito‐Alonso
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCAUSA
- Department of BiologyStanford UniversityStanfordCAUSA
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Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. FORESTS 2021. [DOI: 10.3390/f12050569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.
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Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis. FORESTS 2021. [DOI: 10.3390/f12030364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.
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