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Comita LS, Jones FA, Manzané-Pinzón EJ, Álvarez-Casino L, Cerón-Souza I, Contreras B, Jaén-Barrios N, Ferro N, Engelbrecht BMJ. Limited intraspecific variation in drought resistance along a pronounced tropical rainfall gradient. Proc Natl Acad Sci U S A 2024; 121:e2316971121. [PMID: 38809703 DOI: 10.1073/pnas.2316971121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/08/2024] [Indexed: 05/31/2024] Open
Abstract
Assessing within-species variation in response to drought is crucial for predicting species' responses to climate change and informing restoration and conservation efforts, yet experimental data are lacking for the vast majority of tropical tree species. We assessed intraspecific variation in response to water availability across a strong rainfall gradient for 16 tropical tree species using reciprocal transplant and common garden field experiments, along with measurements of gene flow and key functional traits linked to drought resistance. Although drought resistance varies widely among species in these forests, we found little evidence for within-species variation in drought resistance. For the majority of functional traits measured, we detected no significant intraspecific variation. The few traits that did vary significantly between drier and wetter origins of the same species all showed relationships opposite to expectations based on drought stress. Furthermore, seedlings of the same species originating from drier and wetter sites performed equally well under drought conditions in the common garden experiment and at the driest transplant site. However, contrary to expectation, wetter-origin seedlings survived better than drier-origin seedlings under wetter conditions in both the reciprocal transplant and common garden experiment, potentially due to lower insect herbivory. Our study provides the most comprehensive picture to date of intraspecific variation in tropical tree species' responses to water availability. Our findings suggest that while drought plays an important role in shaping species composition across moist tropical forests, its influence on within-species variation is limited.
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Affiliation(s)
- Liza S Comita
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT 06511
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
| | - F Andrew Jones
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - Eric J Manzané-Pinzón
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
- Departamento de Ciencias Naturales, Facultad de Ciencias y Tecnología, Universidad Tecnológica de Panamá, Panama City, Panamá
| | - Leonor Álvarez-Casino
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
- Department of Plant Ecology, Center for Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Ivania Cerón-Souza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
- Centro de Investigación Tibaitatá, Mosquera Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Cundinamarca 250047, Colombia
| | - Blexein Contreras
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
| | - Nelson Jaén-Barrios
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas CEP 13083-970, SP, Brazil
| | - Natalie Ferro
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
| | - Bettina M J Engelbrecht
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092, Panama City, Panamá
- Department of Plant Ecology, Center for Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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2
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Robert E, Lenz P, Bergeron Y, de Lafontaine G, Bouriaud O, Isabel N, Girardin MP. Future carbon sequestration potential in a widespread transcontinental boreal tree species: Standing genetic variation matters! GLOBAL CHANGE BIOLOGY 2024; 30:e17347. [PMID: 38822663 DOI: 10.1111/gcb.17347] [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: 09/01/2023] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/03/2024]
Abstract
Climate change (CC) necessitates reforestation/afforestation programs to mitigate its impacts and maximize carbon sequestration. But comprehending how tree growth, a proxy for fitness and resilience, responds to CC is critical to maximize these programs' effectiveness. Variability in tree response to CC across populations can notably be influenced by the standing genetic variation encompassing both neutral and adaptive genetic diversity. Here, a framework is proposed to assess tree growth potential at the population scale while accounting for standing genetic variation. We applied this framework to black spruce (BS, Picea mariana [Mill] B.S.P.), with the objectives to (1) determine the key climate variables having impacted BS growth response from 1974 to 2019, (2) examine the relative roles of local adaptation and the phylogeographic structure in this response, and (3) project BS growth under two Shared Socioeconomic Pathways while taking standing genetic variation into account. We modeled growth using a machine learning algorithm trained with dendroecological and genetic data obtained from over 2600 trees (62 populations divided in three genetic clusters) in four 48-year-old common gardens, and simulated growth until year 2100 at the common garden locations. Our study revealed that high summer and autumn temperatures negatively impacted BS growth. As a consequence of warming, this species is projected to experience a decline in growth by the end of the century, suggesting maladaptation to anticipated CC and a potential threat to its carbon sequestration capacity. This being said, we observed a clear difference in response to CC within and among genetic clusters, with the western cluster being more impacted than the central and eastern clusters. Our results show that intraspecific genetic variation, notably associated with the phylogeographic structure, must be considered when estimating the response of widespread species to CC.
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Affiliation(s)
- Etienne Robert
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| | - Patrick Lenz
- Natural Resources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, Quebec City, Quebec, Canada
| | - Yves Bergeron
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Quebec, Canada
- Institut de Recherche Sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, Québec, Canada
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Olivier Bouriaud
- Ștefan Cel Mare University of Suceava, Suceava, Romania
- IGN, ENSG, Laboratoire d'Inventaire Forestier - LIF, Nancy, France
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| | - Martin P Girardin
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada
- Institut de Recherche Sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, Québec, Canada
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3
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Wesselkamp M, Roberts DR, Dormann CF. Identifying potential provenances for climate-change adaptation using spatially variable coefficient models. BMC Ecol Evol 2024; 24:70. [PMID: 38807083 DOI: 10.1186/s12862-024-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials can take decades, hence any approach that supports focussing on a likely set of candidates may save time and money. We use a non-stationary statistical analysis with spatially varying coefficients to identify ecotypes that indicate first regions of similarly adapted varieties of Douglas-fir (Pseudotsuga menziesii (Mirbel) Franco) in North America. For over 70,000 plot-level presence-absences, spatial differences in the survival response to climatic conditions are identified. RESULTS The spatially-variable coefficient model fits the data substantially better than a stationary, i.e. constant-effect analysis (as measured by AIC to account for differences in model complexity). Also, clustering the model terms identifies several potential ecotypes that could not be derived from clustering climatic conditions itself. Comparing these six identified ecotypes to known genetically diverging regions shows some congruence, as well as some mismatches. However, comparing ecotypes among each other, we find clear differences in their climate niches. CONCLUSION While our approach is data-demanding and computationally expensive, with the increasing availability of data on species distributions this may be a useful first screening step during the search for climate-change adapted varieties. With our unsupervised learning approach being explorative, finely resolved genotypic data would be helpful to improve its quantitative validation.
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Affiliation(s)
- Marieke Wesselkamp
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany.
| | - David R Roberts
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
- InnoTech Alberta, 3608 - 33 Street NW, Calgary, AB, T2L 2A6, Canada
- Alberta Biodiversity Monitoring Institute, 1-107 Centennial Centre for Interdisciplinary Studies (CCIS), University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Carsten F Dormann
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
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4
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Blumstein M. The drivers of intraspecific trait variation and their implications for future tree productivity and survival. AMERICAN JOURNAL OF BOTANY 2024:e16312. [PMID: 38576091 DOI: 10.1002/ajb2.16312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
Forests are facing unprecedented levels of stress from pest and disease outbreaks, disturbance, fragmentation, development, and a changing climate. These selective agents act to alter forest composition from regional to cellular levels. Thus, a central challenge for understanding how forests will be impacted by future change is how to integrate across scales of biology. Phenotype, or an observable trait, is the product of an individual's genes (G) and the environment in which an organism lives (E). To date, researchers have detailed how environment drives variation in tree phenotypes over long time periods (e.g., long-term ecological research sites [LTERs]) and across large spatial scales (e.g., flux network). In parallel, researchers have discovered the genes and pathways that govern phenotypes, finding high degrees of genetic control and signatures of local adaptation in many plant traits. However, the research in these two areas remain largely independent of each other, hindering our ability to generate accurate predictions of plant response to environment, an increasingly urgent need given threats to forest systems. I present the importance of both genes and environment in determining tree responses to climate stress. I highlight why the difference between G versus E in driving variation is critical for our understanding of climate responses, then propose means of accelerating research that examines G and E simultaneously by leveraging existing long-term, large-scale phenotypic data sets from ecological networks and adding newly affordable sequence (-omics) data to both drill down to find the genes and alleles influencing phenotypes and scale up to find how patterns of demography and local adaptation may influence future response to change.
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Affiliation(s)
- Meghan Blumstein
- Harvard Forest, Harvard University, Petersham, 01366, MA, USA
- Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, 02139, MA, USA
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5
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Lind BM, Candido-Ribeiro R, Singh P, Lu M, Obreht Vidakovic D, Booker TR, Whitlock MC, Yeaman S, Isabel N, Aitken SN. How useful are genomic data for predicting maladaptation to future climate? GLOBAL CHANGE BIOLOGY 2024; 30:e17227. [PMID: 38558300 DOI: 10.1111/gcb.17227] [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: 02/17/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 04/04/2024]
Abstract
Methods using genomic information to forecast potential population maladaptation to climate change or new environments are becoming increasingly common, yet the lack of model validation poses serious hurdles toward their incorporation into management and policy. Here, we compare the validation of maladaptation estimates derived from two methods-Gradient Forests (GFoffset) and the risk of non-adaptedness (RONA)-using exome capture pool-seq data from 35 to 39 populations across three conifer taxa: two Douglas-fir varieties and jack pine. We evaluate sensitivity of these algorithms to the source of input loci (markers selected from genotype-environment associations [GEA] or those selected at random). We validate these methods against 2- and 52-year growth and mortality measured in independent transplant experiments. Overall, we find that both methods often better predict transplant performance than climatic or geographic distances. We also find that GFoffset and RONA models are surprisingly not improved using GEA candidates. Even with promising validation results, variation in model projections to future climates makes it difficult to identify the most maladapted populations using either method. Our work advances understanding of the sensitivity and applicability of these approaches, and we discuss recommendations for their future use.
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Affiliation(s)
- Brandon M Lind
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rafael Candido-Ribeiro
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Dragana Obreht Vidakovic
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Quebec, Canada
| | - Sally N Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Wan JSH, Bonser SP, Pang CK, Fazlioglu F, Rutherford S. Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies? Ecol Lett 2024; 27:e14419. [PMID: 38613177 DOI: 10.1111/ele.14419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.
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Affiliation(s)
- Justin S H Wan
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Stephen P Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales (UNSW), Sydney, New South Wales, Australia
| | - Clara K Pang
- PlantClinic, Australian Institute of Botanical Science, Royal Botanic Garden, Sydney, New South Wales, Australia
| | | | - Susan Rutherford
- Center for Sustainable Environmental and Ecosystem Research, Department of Environmental Science, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Department of Environmental and Sustainability Sciences, The Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, New Jersey, USA
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, China
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7
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Duffy KJ. The enigma of genetic adaptation in a panmictic pine. THE NEW PHYTOLOGIST 2024. [PMID: 38520184 DOI: 10.1111/nph.19710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Affiliation(s)
- Karl J Duffy
- Department of Biology, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, 80126, Italy
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8
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Zhao W, Gao J, Hall D, Andersson BA, Bruxaux J, Tomlinson KW, Drouzas AD, Suyama Y, Wang XR. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. THE NEW PHYTOLOGIST 2024. [PMID: 38515228 DOI: 10.1111/nph.19694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.
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Affiliation(s)
- Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - David Hall
- Forestry Research Institute of Sweden (Skogforsk), Sävar, SE-91833, Sweden
| | - Bea Angelica Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Kyle W Tomlinson
- Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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9
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Zeng ZA, Wolkovich EM. Weak evidence of provenance effects in spring phenology across Europe and North America. THE NEW PHYTOLOGIST 2024. [PMID: 38494441 DOI: 10.1111/nph.19674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
Forecasting the biological impacts of climate change requires understanding how species respond to warmer temperatures through interannual flexible variation vs through adaptation to local conditions. Yet, we often lack this information entirely or find conflicting evidence across studies, which is the case for spring phenology. We synthesized common garden studies across Europe and North America that reported spring event dates for a mix of angiosperm and gymnosperm tree species in the northern hemisphere, capturing data from 384 North American and 101 European provenances (i.e. populations) with observations from 1962 to 2019, alongside autumn event data when provided. Across continents, we found no evidence of provenance effects in spring phenology, but strong clines with latitude and mean annual temperature in autumn. These effects, however, appeared to diverge by continent and species type (gymnosperm vs angiosperm), with particularly pronounced clines in North America in autumn events. Our results suggest flexible, likely plastic responses, in spring phenology with warming, and potential limits - at least in the short term - due to provenance effects for autumn phenology. They also highlight that, after over 250 yr of common garden studies on tree phenology, we still lack a holistic predictive model of clines across species and phenological events.
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Affiliation(s)
- Ziyun Alina Zeng
- Forest Resources Management, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Elizabeth M Wolkovich
- Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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10
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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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11
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Bruxaux J, Zhao W, Hall D, Curtu AL, Androsiuk P, Drouzas AD, Gailing O, Konrad H, Sullivan AR, Semerikov V, Wang XR. Scots pine - panmixia and the elusive signal of genetic adaptation. THE NEW PHYTOLOGIST 2024. [PMID: 38308133 DOI: 10.1111/nph.19563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
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Affiliation(s)
- Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
- Forestry Research Institute of Sweden (Skogforsk), 918 21, Sävar, Sweden
| | | | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Heino Konrad
- Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), 1140, Vienna, Austria
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, 620144, Ekaterinburg, Russia
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
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12
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Danusevičius D, Rajora OP, Kavaliauskas D, Baliuckas V, Augustaitis A. Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring. Sci Rep 2024; 14:2713. [PMID: 38302512 PMCID: PMC10834436 DOI: 10.1038/s41598-024-52769-y] [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: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012-0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.
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Affiliation(s)
- Darius Danusevičius
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, PO Box 4400, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada.
| | - Darius Kavaliauskas
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania
- Lithuanian Research Centre for Agriculture and Forestry, Forestry Institute, Liepu Str. 1, 53101, Kaunas Reg., Lithuania
| | - Virgilijus Baliuckas
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania
- Lithuanian Research Centre for Agriculture and Forestry, Forestry Institute, Liepu Str. 1, 53101, Kaunas Reg., Lithuania
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Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
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Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Otte KA. A window into local adaptation. Mol Ecol Resour 2024; 24:e13872. [PMID: 37772701 DOI: 10.1111/1755-0998.13872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023]
Abstract
How organisms adapt to their environment is not only a central topic of evolutionary biology but also a pressing question in the light of recent global change. Unravelling the genetic basis of these local adaptations can help to predict the response of a population to an increase in temperature or the more frequent occurrence of droughts. A popular approach to study the genes that drive local adaptation is the analysis of genotype-environment associations (GEA), testing the correlation of genomic features (typically single-nucleotide polymorphisms, SNPs) and environmental conditions. In this issue of Molecular Ecology Resources, Booker et al. (Molecular Ecology Resources, 2023) present a new approach to GEA, introducing genomic window analysis. They combine the information of neighbouring SNPs instead of analysing each SNP independently, therefore gaining power for detecting genomic signals of environmental adaptation. Using simulations of local adaptation to a heterogeneous environment as well as previously published real data from a natural population of lodgepole pine, they prove the superiority of their method over several established GEA approaches, especially in the case of small sample sizes. Leveraging the information present in closely linked genomic sites, Booker et al. (Molecular Ecology Resources, 2023) take genotype-environment association studies to the next level.
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Affiliation(s)
- Kathrin A Otte
- Institute of Cell and Systems Biology of Animals, Population Genomics, Universität Hamburg, Hamburg, Germany
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15
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Meger J, Ulaszewski B, Chmura DJ, Burczyk J. Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur. BMC Genomics 2024; 25:78. [PMID: 38243199 PMCID: PMC10797717 DOI: 10.1186/s12864-023-09897-y] [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: 02/27/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change. RESULTS Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 FST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change. CONCLUSIONS The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Daniel J Chmura
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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Alía R, Climent J, Santos-Del-Blanco L, Gonzalez-Arrojo A, Feito I, Grivet D, Majada J. Adaptive potential of maritime pine under contrasting environments. BMC PLANT BIOLOGY 2024; 24:37. [PMID: 38191282 PMCID: PMC10775667 DOI: 10.1186/s12870-023-04687-w] [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: 04/28/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Predicting the adaptability of forest tree populations under future climates requires a better knowledge of both the adaptive significance and evolvability of measurable key traits. Phenotypic plasticity, standing genetic variation and degree of phenotypic integration shape the actual and future population genetic structure, but empirical estimations in forest tree species are still extremely scarce. We analysed 11 maritime pine populations covering the distribution range of the species (119 families and 8 trees/family, ca. 1300 trees) in a common garden experiment planted at two sites with contrasting productivity. We used plant height as a surrogate of fitness and measured five traits (mean and plasticity of carbon isotope discrimination, specific leaf area, needle biomass, Phenology growth index) related to four different strategies (acquisitive economics, photosynthetic organ size, growth allocation and avoidance of water stress). RESULTS Estimated values of additive genetic variation would allow adaptation of the populations to future environmental conditions. Overall phenotypic integration and selection gradients were higher at the high productivity site, while phenotypic integration within populations was higher at the low productivity site. Response to selection was related mainly to photosynthetic organ size and drought-avoidance mechanisms rather than to water use efficiency. Phenotypic plasticity of water use efficiency could be maladaptive, resulting from selection for height growth. CONCLUSIONS Contrary to the expectations in a drought tolerant species, our study suggests that variation in traits related to photosynthetic organ size and acquisitive investment of resources drive phenotypic selection across and within maritime pine populations. Both genetic variation and evolvability of key adaptive traits were considerably high, including plasticity of water use efficiency. These characteristics would enable a relatively fast micro-evolution of populations in response to the ongoing climate changes. Moreover, differentiation among populations in the studied traits would increase under the expected more productive future Atlantic conditions.
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Affiliation(s)
- Ricardo Alía
- Instituto de Ciencias Forestales, ICIFOR-INIA, CSIC, Madrid, 28040, Spain.
| | - Jose Climent
- Instituto de Ciencias Forestales, ICIFOR-INIA, CSIC, Madrid, 28040, Spain
| | | | | | | | - Delphine Grivet
- Instituto de Ciencias Forestales, ICIFOR-INIA, CSIC, Madrid, 28040, Spain
| | - Juan Majada
- Forest and Wood Technology Research Centre (CETEMAS), Carbayin, 33936, Spain
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Aihara T, Araki K, Onuma Y, Cai Y, Paing AMM, Goto S, Hisamoto Y, Tomaru N, Homma K, Takagi M, Yoshida T, Iio A, Nagamatsu D, Kobayashi H, Hirota M, Uchiyama K, Tsumura Y. Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges. Heredity (Edinb) 2023; 131:387-397. [PMID: 37940658 PMCID: PMC10673911 DOI: 10.1038/s41437-023-00655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii's distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations' saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.
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Affiliation(s)
- Takaki Aihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kyoko Araki
- Garden Division, Maintenance and Works Department, the Imperial Household Agency, 1-1, Chiyoda, Chiyoda-ku, Tokyo, 100-8111, Japan
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yunosuke Onuma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yihan Cai
- Graduate School of Environmental Science, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Aye Myat Myat Paing
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Susumu Goto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Hisamoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Cikusa-ku, Nagoya, Aichi, 464-0804, Japan
| | - Kosuke Homma
- Sado Island Center for Ecological Sustainability, Niigata University, 1101-1, Niibokatagami, Sado, Niigata, 952-0103, Japan
| | - Masahiro Takagi
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen kibanadai nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Toshiya Yoshida
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Atsuhiro Iio
- Graduate School of Integrated Science and Technology, Shizuoka University, 836, Ohtani, Suruga-ku, Shizuoka, Shizuoka, 422-8017, Japan
| | - Dai Nagamatsu
- Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Tottori, Tottori, 680-8553, Japan
| | - Hajime Kobayashi
- Faculty of Agriculture, Shinshu University, 8304, Minamiminowa-mura, Kamiina-gun, Nagano, 399-4598, Japan
| | - Mitsuru Hirota
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1, Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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18
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Silvestro R, Mura C, Alano Bonacini D, de Lafontaine G, Faubert P, Mencuccini M, Rossi S. Local adaptation shapes functional traits and resource allocation in black spruce. Sci Rep 2023; 13:21257. [PMID: 38040772 PMCID: PMC10692160 DOI: 10.1038/s41598-023-48530-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Climate change is rapidly altering weather patterns, resulting in shifts in climatic zones. The survival of trees in specific locations depends on their functional traits. Local populations exhibit trait adaptations that ensure their survival and accomplishment of growth and reproduction processes during the growing season. Studying these traits offers valuable insights into species responses to present and future environmental conditions, aiding the implementation of measures to ensure forest resilience and productivity. This study investigates the variability in functional traits among five black spruce (Picea mariana (Mill.) B.S.P.) provenances originating from a latitudinal gradient along the boreal forest, and planted in a common garden in Quebec, Canada. We examined differences in bud phenology, growth performance, lifetime first reproduction, and the impact of a late-frost event on tree growth and phenological adjustments. The findings revealed that trees from northern sites exhibit earlier budbreak, lower growth increments, and reach reproductive maturity earlier than those from southern sites. Late-frost damage affected growth performance, but no phenological adjustment was observed in the successive year. Local adaptation in the functional traits may lead to maladaptation of black spruce under future climate conditions or serve as a potent evolutionary force promoting rapid adaptation under changing environmental conditions.
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Affiliation(s)
- R Silvestro
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada.
| | - C Mura
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
| | - D Alano Bonacini
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
| | - G de Lafontaine
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de biologie, chimie et Géographie, Centre for Northern Studies, Centre for Forest Research, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - P Faubert
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
- Carbone boréal, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H 2B1, Canada
| | - M Mencuccini
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), 08193, Bellaterra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluis Companys 23, 08010, Barcelona, Spain
| | - S Rossi
- Laboratoire sur les écosystèmes terrestres boréaux, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
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19
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Chen T, Xu J, Wang L, Wang H, You E, Deng C, Bian H, Shen Y. Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau. Heredity (Edinb) 2023; 131:316-326. [PMID: 37935814 PMCID: PMC10673939 DOI: 10.1038/s41437-023-00647-0] [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: 12/05/2022] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 11/09/2023] Open
Abstract
Understanding the local adaptation of crops has long been a concern of evolutionary biologists and molecular ecologists. Identifying the adaptive genetic variability in the genome is crucial not only to provide insights into the genetic mechanism of local adaptation but also to explore the adaptation potential of crops. This study aimed to identify the climatic drivers of naked barley landraces and putative adaptive loci driving local adaptation on the Qinghai-Tibetan Plateau (QTP). To this end, a total of 157 diverse naked barley accessions were genotyped using the genotyping-by-sequencing approach, which yielded 3123 high-quality SNPs for population structure analysis and partial redundancy analysis, and 37,636 SNPs for outlier analysis. The population structure analysis indicated that naked barley landraces could be divided into four groups. We found that the genomic diversity of naked barley landraces could be partly traced back to the geographical and environmental diversity of the landscape. In total, 136 signatures associated with temperature, precipitation, and ultraviolet radiation were identified, of which 13 had pleiotropic effects. We mapped 447 genes, including a known gene HvSs1. Some genes involved in cold stress and regulation of flowering time were detected near eight signatures. Taken together, these results highlight the existence of putative adaptive loci in naked barley on QTP and thus improve our current understanding of the genetic basis of local adaptation.
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Affiliation(s)
- Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Deng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Bian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China.
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20
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James J, Kastally C, Budde KB, González-Martínez SC, Milesi P, Pyhäjärvi T, Lascoux M. Between but Not Within-Species Variation in the Distribution of Fitness Effects. Mol Biol Evol 2023; 40:msad228. [PMID: 37832225 PMCID: PMC10630145 DOI: 10.1093/molbev/msad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/04/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.
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Affiliation(s)
- Jennifer James
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Swedish Collegium of Advanced Study, Uppsala University, Uppsala, Sweden
| | - Chedly Kastally
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Katharina B Budde
- Department of Forest Genetics and Forest Tree Breeding, Georg-August-University Goettingen, Goettingen, Germany
- Center of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Goettingen, Germany
| | - Santiago C González-Martínez
- National Research Institute for Agriculture, Food and the Environment (INRAE), University of Bordeaux, BIOGECO, Cestas, France
| | - Pascal Milesi
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Martin Lascoux
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Vasey GL, Urza AK, Chambers JC, Pringle EG, Weisberg PJ. Clinal variations in seedling traits and responses to water availability correspond to seed-source environmental gradients in a foundational dryland tree species. ANNALS OF BOTANY 2023; 132:203-216. [PMID: 36905361 PMCID: PMC10583205 DOI: 10.1093/aob/mcad041] [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: 11/14/2022] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS In dryland ecosystems, conifer species are threatened by more frequent and severe droughts, which can push species beyond their physiological limits. Adequate seedling establishment will be critical for future resilience to global change. We used a common garden glasshouse experiment to determine how seedling functional trait expression and plasticity varied among seed sources in response to a gradient of water availability, focusing on a foundational dryland tree species of the western USA, Pinus monophylla. We hypothesized that the expression of growth-related seedling traits would show patterns consistent with local adaptation, given clinal variation among seed source environments. METHODS We collected P. monophylla seeds from 23 sites distributed across rangewide gradients of aridity and seasonal moisture availability. A total of 3320 seedlings were propagated with four watering treatments representing progressively decreasing water availability. Above- and below-ground growth-related traits of first-year seedlings were measured. Trait values and trait plasticity, here representing the degree of variation among watering treatments, were modelled as a function of watering treatment and environmental conditions at the seed source locations (i.e. water availability, precipitation seasonality). KEY RESULTS We found that, under all treatments, seedlings from more arid climates had larger above- and below-ground biomass compared to seedlings from sites experiencing lower growing-season water limitation, even after accounting for differences in seed size. Additionally, trait plasticity in response to watering treatments was greatest for seedlings from summer-wet sites that experience periodic monsoonal rain events. CONCLUSIONS Our results show that P. monophylla seedlings respond to drought through plasticity in multiple traits, but variation in trait responses suggests that different populations are likely to respond uniquely to changes in local climate. Such trait diversity will probably influence the potential for future seedling recruitment in woodlands that are projected to experience extensive drought-related tree mortality.
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Affiliation(s)
- Georgia L Vasey
- Department of Natural Resources and Environmental Science, University of Nevada Reno, 1664 N. Virginia Street, Mail Stop 186, Reno, NV 89557, USA
| | - Alexandra K Urza
- USDA Forest Service, Rocky Mountain Research Station, 920 Valley Road, Reno, NV 89512, USA
| | - Jeanne C Chambers
- USDA Forest Service, Rocky Mountain Research Station, 920 Valley Road, Reno, NV 89512, USA
| | - Elizabeth G Pringle
- Department of Biology, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, 1664 N. Virginia Street, Mail Stop 0314, Reno, NV 89557, USA
| | - Peter J Weisberg
- Department of Natural Resources and Environmental Science, University of Nevada Reno, 1664 N. Virginia Street, Mail Stop 186, Reno, NV 89557, USA
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22
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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23
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Petak C, Frati L, Brennan RS, Pespeni MH. Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins. Am Nat 2023; 202:571-586. [PMID: 37792925 DOI: 10.1086/726013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
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24
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Li P, Xiao L, Du Q, Quan M, Song Y, He Y, Huang W, Xie J, Lv C, Wang D, Zhou J, Li L, Liu Q, El‐Kassaby YA, Zhang D. Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2002-2018. [PMID: 37392407 PMCID: PMC10502748 DOI: 10.1111/pbi.14108] [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: 02/14/2023] [Revised: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.
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Affiliation(s)
- Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuepeng Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuling He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Weixiong Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jianbo Xie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Dan Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qing Liu
- CSIRO Agriculture and Food, Black MountainCanberraAustralian Capital TerritoryAustralia
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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25
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de la Mata R, Zas R. Plasticity in growth is genetically variable and highly conserved across spatial scales in a Mediterranean pine. THE NEW PHYTOLOGIST 2023; 240:542-554. [PMID: 37491863 DOI: 10.1111/nph.19158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023]
Abstract
Phenotypic plasticity is a main mechanism for sessile organisms to cope with changing environments. Plasticity is genetically based and can evolve under natural selection so that populations within a species show distinct phenotypic responses to environment. An important question that remains elusive is whether the intraspecific variation in plasticity at different spatial scales is independent from each other. To test whether variation in plasticity to macro- and micro-environmental variation is related among each other, we used growth data of 25 Pinus pinaster populations established in seven field common gardens in NW Spain. Phenotypic plasticity to macro-environmental variation was estimated across test sites while plasticity to micro-environmental variation was estimated by using semivariography and kriging for modeling within-site heterogeneity. We provide empirical evidence of among-population variation in the magnitude of plastic responses to both micro- and macro-environmental variation. Importantly, we found that such responses were positively correlated across spatial scales. Selection for plasticity at one scale of environmental variation may impact the expression of plasticity at other scales, having important consequences on the ability of populations to buffer climate change. These results improve our understanding of the ecological drivers underlying the expression of phenotypic plasticity.
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Affiliation(s)
- Raul de la Mata
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (EBD-CSIC), Sevilla, Andalucía, 41092, Spain
| | - Rafael Zas
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, Pontevedra, 36080, Spain
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26
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Hankin LE, Leger EA, Bisbing SM. Reforestation of high elevation pines: Direct seeding success depends on seed source and sowing environment. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2897. [PMID: 37305925 DOI: 10.1002/eap.2897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/10/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Forest persistence in regions impacted by increasing water and temperature stress will depend upon species' ability to either rapidly adjust to novel conditions or migrate to track ecological niches. Predicted, rapid climate change is likely to outpace the adaptive and migratory capacity of long-lived isolated tree species, and reforestation may be critical to species' persistence. Facilitating persistence both within and beyond a species' range requires identification of seed lots best adapted to the current and future conditions predicted with rapid climate change. We evaluate variation in emergent seedling performance that leads to differential survival among species and populations for three high elevation five-needle pines. We paired a fully reciprocal field common garden experiment with a greenhouse common garden study to (1) quantify variation in seedling emergence and functional traits, (2) ask how functional traits affect performance under different establishment conditions, and (3) evaluate whether trait and performance variation demonstrates local adaptation and plasticity. Among study species-limber, Great Basin bristlecone, and whitebark pines-we found divergence in emergence and functional traits, though soil moisture was the strongest driver of seedling emergence and abundance across all species. Generalist limber pine had a clear emergence advantage as well as traits associated with drought adaptation, while edaphic specialist bristlecone pine was characterized by low emergence yet high early survival once established. Despite evidence for edaphic specialization, soil characteristics alone did not explain bristlecone success. Across species, trait-environment relationships provided some evidence for local adaptation in drought-adapted traits, but we found no evidence of local adaptation in emergence or survival at this early life stage. For managers looking to promote persistence, sourcing seed from drier environments is likely to impart greater drought resistance into reforestation efforts through strategies such as greater root investment, increasing the probability of early seedling survival. This research demonstrates, through a rigorous reciprocal transplant experimental design, that it may be possible to select climate- and soil-appropriate seed sources for reforestation. However, planting success will ultimately rely on a suitable establishment environment, requiring careful consideration of interannual climate variability for management interventions in these climate and disturbance-impacted tree species.
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Affiliation(s)
- Lacey E Hankin
- Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno, Nevada, USA
- Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Elizabeth A Leger
- Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
- Department of Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Sarah M Bisbing
- Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno, Nevada, USA
- Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
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27
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Soularue JP, Firmat C, Caignard T, Thöni A, Arnoux L, Delzon S, Ronce O, Kremer A. Antagonistic Effects of Assortative Mating on the Evolution of Phenotypic Plasticity along Environmental Gradients. Am Nat 2023; 202:18-39. [PMID: 37384769 PMCID: PMC7614710 DOI: 10.1086/724579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractPrevious theory has shown that assortative mating for plastic traits can maintain genetic divergence across environmental gradients despite high gene flow. Yet these models did not examine how assortative mating affects the evolution of plasticity. We here describe patterns of genetic variation across elevation for plasticity in a trait under assortative mating, using multiple-year observations of budburst date in a common garden of sessile oaks. Despite high gene flow, we found significant spatial genetic divergence for the intercept, but not for the slope, of reaction norms to temperature. We then used individual-based simulations, where both the slope and the intercept of the reaction norm evolve, to examine how assortative mating affects the evolution of plasticity, varying the intensity and distance of gene flow. Our model predicts the evolution of either suboptimal plasticity (reaction norms with a slope shallower than optimal) or hyperplasticity (slopes steeper than optimal) in the presence of assortative mating when optimal plasticity would evolve under random mating. Furthermore, a cogradient pattern of genetic divergence for the intercept of the reaction norm (where plastic and genetic effects are in the same direction) always evolves in simulations with assortative mating, consistent with our observations in the studied oak populations.
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28
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Filipe JC, Ahrens CC, Byrne M, Hardy G, Rymer PD. Germination temperature sensitivity differs between co-occurring tree species and climate origins resulting in contrasting vulnerability to global warming. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:146-162. [PMID: 37362420 PMCID: PMC10290426 DOI: 10.1002/pei3.10108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/20/2023] [Accepted: 04/04/2023] [Indexed: 06/28/2023]
Abstract
Climate change is shifting temperatures from historical patterns, globally impacting forest composition and resilience. Seed germination is temperature-sensitive, making the persistence of populations and colonization of available habitats vulnerable to warming. This study assessed germination response to temperature in foundation trees in south-western Australia's Mediterranean-type climate forests (Eucalyptus marginata (jarrah) and Corymbia calophylla (marri)) to estimate the thermal niche and vulnerability among populations. Seeds from the species' entire distribution were collected from 12 co-occurring populations. Germination thermal niche was investigated using a thermal gradient plate (5-40°C). Five constant temperatures between 9 and 33°C were used to test how the germination niche (1) differs between species, (2) varies among populations, and (3) relates to the climate of origin. Germination response differed among species; jarrah had a lower optimal temperature and thermal limit than marri (T o 15.3°C, 21.2°C; ED50 23.4°C, 31°C, respectively). The thermal limit for germination differed among populations within both species, yet only marri showed evidence for adaptation to thermal origins. While marri has the capacity for germination at higher thermal temperatures, jarrah is more vulnerable to global warming exceeding safety margins. This discrepancy is predicted to alter species distributions and forest composition in the future.
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Affiliation(s)
- João C. Filipe
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
- Centre for Terrestrial Ecosystem Science and SustainabilityHarry Butler InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Collin C. Ahrens
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Research Centre for Ecosystem ResilienceRoyal Botanic Gardens and Domain TrustSydneyNew South WalesAustralia
- Cesar AustraliaBrunswickVictoriaAustralia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
| | - Giles Hardy
- Centre for Terrestrial Ecosystem Science and SustainabilityHarry Butler InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Paul D. Rymer
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
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29
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Archambeau J, Benito Garzón M, de Miguel M, Brachi B, Barraquand F, González-Martínez SC. Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine. Heredity (Edinb) 2023:10.1038/s41437-023-00622-9. [PMID: 37221230 DOI: 10.1038/s41437-023-00622-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023] Open
Abstract
How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.
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Affiliation(s)
- Juliette Archambeau
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, UK.
| | | | - Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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30
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Yu X, Wei P, Zhao S, Chen Z, Li X, Zhang W, Liu C, Yang Y, Li X, Liu X. Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau. PLANT CELL REPORTS 2023; 42:879-893. [PMID: 36973418 DOI: 10.1007/s00299-023-03005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Shuqi Zhao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinzhong Li
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Wencai Zhang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China.
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31
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Beiter CM, Crimmins TM. How consistently do species leaf-out or flower in the same order? Understanding the factors that shape this characteristic of plant communities. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023:10.1007/s00484-023-02477-5. [PMID: 37186257 DOI: 10.1007/s00484-023-02477-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Plant species are frequently reported to undergo leaf-out and flowering in a consistent order from 1 year to the next; however, only a limited number of these findings arise from studies encompassing many species or sites. Here, we evaluate the consistency in the order species leafed out in the northeastern United States using observations contributed to the USA National Phenology Network's Nature's Notebook platform. We repeated this analysis for flowering, evaluating a total of 132 species across 84 sites. We documented a relatively high degree of consistency in the order of both events among individual plants, with higher consistency in flowering. A small number of species pairs exhibited very high consistency in phenological order across several sites. The majority of species pairs exhibited variability in how consistently they underwent either leaf-out or flowering from site to site, which could be the result of either plastic or locally adaptive responses. Our investigation revealed that neither functional type nor seasonal position played a major role in shaping how consistently species leafed out or flowered in the same order. Instead, we found the number of days separating the events and interannual variability in timing to be the most influential factors driving the consistency in ordering.
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Affiliation(s)
- Caryn M Beiter
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA.
| | - Theresa M Crimmins
- USA National Phenology Network, School of Natural Resources and the Environment University of Arizona, 1311 E. 4Th. St., Suite 325, Tucson, AZ, 85721, USA
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Assaeed AM, Dar BA, Al-Doss AA, Al-Rowaily SL, Malik JA, Abd-ElGawad AM. Phenotypic Plasticity Strategy of Aeluropus lagopoides Grass in Response to Heterogenous Saline Habitats. BIOLOGY 2023; 12:biology12040553. [PMID: 37106753 PMCID: PMC10135548 DOI: 10.3390/biology12040553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
Understanding the response variation of morphological parameters and biomass allocation of plants in heterogeneous saline environments is helpful in evaluating the internal correlation between plant phenotypic plasticity mechanism and biomass allocation. The plasticity of plants alters the interaction among individuals and their environment and consequently affects the population dynamics and aspects of community and ecosystem functioning. The current study aimed to assess the plasticity of Aeluropus lagopoides traits with variation in saline habitats. Understanding the habitat stress tolerance strategy of A. lagopoides is of great significance since it is one of the highly palatable forage grass in the summer period. Five different saline flat regions (coastal and inland) within Saudi Arabia were targeted, and the soil, as well as the morphological and physiological traits of A. lagopoides, were assessed. Comprehensive correlation analyses were performed to correlate the traits with soil, region, or among each other. The soil analysis revealed significant variation among the five studied regions for all measured parameters, as well as among the soil layers showing the highest values in the upper layer and decreased with the depth. Significant differences were determined for all tested parameters of the morphological and reproductive traits as well as for the biomass allocation of A. lagopoides, except for the leaf thickness. In the highly saline region, Qaseem, A. lagopoides showed stunted aerial growth, high root/shoot ratio, improved root development, and high biomass allocation. In contrast, the populations growing in the low saline region (Jizan) showed the opposite trend. Under the more stressful condition, like in Qaseem and Salwa, A. lagopoides produce low spikes in biomass and seeds per plant, compared to the lowest saline habitats, such as Jouf. There was no significant difference in physiological parameters except stomatal conductance (gs), which is highest in the Jizan region. In conclusion, the population of A. lagopoides is tolerant of harsh environments through phenotypic plasticity. This could be a candidate species to rehabilitate the saline habitats, considering saline agriculture and saline soil remediation.
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Affiliation(s)
- Abdulaziz M Assaeed
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Basharat A Dar
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah A Al-Doss
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saud L Al-Rowaily
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Jahangir A Malik
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed M Abd-ElGawad
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
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Jiménez-Ramírez A, Solé-Medina A, Ramírez-Valiente JA, Robledo-Arnuncio JJ. Microgeographic variation in early fitness traits of Pinus sylvestris from contrasting soils. AMERICAN JOURNAL OF BOTANY 2023; 110:e16159. [PMID: 36943007 DOI: 10.1002/ajb2.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 05/11/2023]
Abstract
PREMISE The possibility of fine-scale intraspecific adaptive divergence under gene flow is established by theoretical models and has been confirmed empirically in tree populations distributed along steep altitudinal clines or across extreme edaphic discontinuities. However, the possibility of microgeographic adaptive divergence due to less severe but more frequent kinds of soil variation is unclear. METHODS In this study, we looked for evidence of local adaptation to calcareous versus siliceous soil types in two nearby Mediterranean Pinus sylvestris populations connected via pollen flow. Using a greenhouse experiment, we tested for variation in early (up to three years of age) seedling performance among open-pollinated maternal families originating from each edaphic provenance when experimentally grown on both types of natural local substrate. RESULTS Although seedlings were clearly affected by the edaphic environment, exhibiting lower and slower emergence as well as higher mortality on the calcareous than in the siliceous substrate, neither the performance on each substrate nor the plasticity among substrates varied significantly with seedling edaphic provenance. CONCLUSIONS We found no evidence of local adaptation to a non-extreme edaphic discontinuity over a small spatial scale, at least during early stages of seedling establishment. Future studies on microgeographic soil-driven adaptation should consider long-term experiments to minimize maternal effects and allow a potentially delayed expression of edaphic adaptive divergence.
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Affiliation(s)
- Azucena Jiménez-Ramírez
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Genetics, Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - Aida Solé-Medina
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José A Ramírez-Valiente
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Ecological and Forestry Applications Research Centre (CREAF), Cerdanyola del Vallès, Spain
| | - Juan J Robledo-Arnuncio
- Instituto de Ciencias Forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ICIFOR-INIA), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Zhang X, Guo R, Shen R, Landis JB, Jiang Q, Liu F, Wang H, Yao X. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. HORTICULTURE RESEARCH 2023; 10:uhad031. [PMID: 37799629 PMCID: PMC10548413 DOI: 10.1093/hr/uhad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/14/2023] [Indexed: 10/07/2023]
Abstract
A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in the southern tropical region of China, occurring in spatially heterogeneous environments. In the present study we combined population genomic, epigenomic, and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient, and to assess genomic offset to climatic change for A. eriantha. The population structure is strongly shaped by geography and influenced by restricted gene flow resulting from isolation by distance due to habitat fragmentation. In total, we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation, which were enriched in functional categories related to development processes and stress response; both temperature and precipitation are important factors driving adaptive variation. In addition to single-nucleotide polymorphisms (SNPs), a total of 27 single-methylation variants (SMVs) had significant correlation with at least one of four climatic variables and 16 SMVs were located in or adjacent to genes, several of which were predicted to be involved in plant response to abiotic or biotic stress. Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change. Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation. Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruinan Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853 USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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Gloy J, Herzschuh U, Kruse S. Evolutionary adaptation of trees and modelled future larch forest extent in Siberia. Ecol Modell 2023; 478:110278. [PMID: 37013221 PMCID: PMC9972785 DOI: 10.1016/j.ecolmodel.2023.110278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/08/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023]
Abstract
With changing climate, the boreal forest could potentially migrate north and become threatened by droughts in the south. However, whether larches, the dominant tree species in eastern Siberia, can adapt to novel situations is largely unknown but is crucial for predicting future population dynamics. Exploring variable traits and trait adaptation through inheritance in an individual-based model can improve our understanding and help future projections. We updated the individual-based spatially explicit vegetation model LAVESI (Larix Vegetation Simulator), used for forest predictions in Eastern Siberia, with trait value variation and incorporated inheritance of parental values to their offspring. Forcing the model with both past and future climate projections, we simulated two areas - the expanding northern treeline and a southerly area experiencing drought. While the specific trait of 'seed weight' regulates migration, the abstract 'drought resistance' protects stands. We show that trait variation with inheritance leads to an increase in migration rate (∼ 3% area increase until 2100). The drought resistance simulations show that, under increasing stress, including adaptive traits leads to larger surviving populations (17% of threatened under RCP 4.5 (Representative Concentration Pathway)). We show that with the increase expected under the RCP 8.5 scenario vast areas (80% of the extrapolated area) of larch forest are threatened and could disappear due to drought as adaptation plays only a minor role under strong warming. We conclude that variable traits facilitate the availability of variants under environmental changes. Inheritance allows populations to adapt to environments and promote successful traits, which leads to populations that can spread faster and be more resilient, provided the changes are not too drastic in both time and magnitude. We show that trait variation and inheritance contribute to more accurate models that can improve our understanding of responses of boreal forests to global change.
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McNichol BH, Russo SE. Plant Species' Capacity for Range Shifts at the Habitat and Geographic Scales: A Trade-Off-Based Framework. PLANTS (BASEL, SWITZERLAND) 2023; 12:1248. [PMID: 36986935 PMCID: PMC10056461 DOI: 10.3390/plants12061248] [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] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Climate change is causing rapid shifts in the abiotic and biotic environmental conditions experienced by plant populations, but we lack generalizable frameworks for predicting the consequences for species. These changes may cause individuals to become poorly matched to their environments, potentially inducing shifts in the distributions of populations and altering species' habitat and geographic ranges. We present a trade-off-based framework for understanding and predicting whether plant species may undergo range shifts, based on ecological strategies defined by functional trait variation. We define a species' capacity for undergoing range shifts as the product of its colonization ability and the ability to express a phenotype well-suited to the environment across life stages (phenotype-environment matching), which are both strongly influenced by a species' ecological strategy and unavoidable trade-offs in function. While numerous strategies may be successful in an environment, severe phenotype-environment mismatches result in habitat filtering: propagules reach a site but cannot establish there. Operating within individuals and populations, these processes will affect species' habitat ranges at small scales, and aggregated across populations, will determine whether species track climatic changes and undergo geographic range shifts. This trade-off-based framework can provide a conceptual basis for species distribution models that are generalizable across plant species, aiding in the prediction of shifts in plant species' ranges in response to climate change.
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Affiliation(s)
- Bailey H. McNichol
- School of Biological Sciences, University of Nebraska–Lincoln, 1101 T Street, 402 Manter Hall, Lincoln, NE 68588-0118, USA;
| | - Sabrina E. Russo
- School of Biological Sciences, University of Nebraska–Lincoln, 1101 T Street, 402 Manter Hall, Lincoln, NE 68588-0118, USA;
- Center for Plant Science Innovation, University of Nebraska–Lincoln, 1901 Vine Street, N300 Beadle Center, Lincoln, NE 68588-0118, USA
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Knott JA, Liang L, Dukes JS, Swihart RK, Fei S. Phenological response to climate variation in a northern red oak plantation: Links to survival and productivity. Ecology 2023; 104:e3940. [PMID: 36457179 DOI: 10.1002/ecy.3940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 12/04/2022]
Abstract
In a changing climate, the future survival and productivity of species rely on individual populations to respond to shifting environmental conditions. Many tree species, including northern red oak (Quercus rubra), exhibit phenotypic plasticity, the ability to respond to changes in environmental conditions at within-generation time scales, through varying traits such as leaf phenology. Phenotypic plasticity of phenology may vary among populations within a species' range, and it is unclear if the range of plasticity is adequate to promote fitness. Here, we used a 58-year-old common garden to test whether northern red oak populations differed in phenological sensitivity to changes in temperature and whether differences in phenological sensitivity were associated with differences in productivity and survival (proxies of fitness). We recorded 8 years of spring leaf emergence and autumn leaf coloration and loss in 28 distinct populations from across the species' full range. Across the 28 populations, spring leaf out consistently advanced in warmer years, but fall phenology was less responsive to changes in temperature. Southern, warm-adapted populations had larger shifts in phenology in response to springtime warming but had lower long-term survival. Moreover, higher phenological sensitivity to spring warming was not strongly linked to increased productivity. Instead, fitness was more closely linked to latitudinal gradients. Although springtime phenological sensitivity to climate change is common across northern red oak populations, responses of productivity and survival, which could determine longer-term trajectories of species abundance, are more variable across the species' range.
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Affiliation(s)
- Jonathan A Knott
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,United States Department of Agriculture, Forest Service, St. Paul, Minnesota, USA
| | - Liang Liang
- Department of Geography, University of Kentucky, Lexington, Kentucky, USA
| | - Jeffrey S Dukes
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Robert K Swihart
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Songlin Fei
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
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Chung MY, Merilä J, Kim Y, Mao K, López‐Pujol J, Chung MG. A review on
Q
ST
–
F
ST
comparisons of seed plants: Insights for conservation. Ecol Evol 2023; 13:e9926. [PMID: 37006890 PMCID: PMC10049885 DOI: 10.1002/ece3.9926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants, regarding both within-population and among-population components. We then introduce the estimates of among-population genetic differentiation in quantitative traits (Q ST) and neutral markers (F ST) to plant biology and summarize conservation applications derived from Q ST-F ST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of NGV and AGV, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, Q ST is about 3.6, 1.5, and 1.1 times greater than F ST in woody plants, annuals, and herbaceous perennials, respectively. Hence, conservation and management policies or suggestions based solely on inference on F ST could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum Q ST rather than average Q ST. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, particularly woody species.
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Affiliation(s)
- Mi Yoon Chung
- Department of Biological SciencesChungnam National UniversityDaejeon34134South Korea
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFI‐00014Finland
- Area of Ecology & BiodiversitySchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Yuseob Kim
- Division of EcoScienceEwha Womans UniversitySeoul03760South Korea
- Department of Life ScienceEwha Womans UniversitySeoul03760South Korea
| | - Kangshan Mao
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of Education, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu610065China
| | - Jordi López‐Pujol
- Botanic Institute of Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelona08038CataloniaSpain
- Universidad Espíritu Santo (UEES)Samborondón091650Ecuador
| | - Myong Gi Chung
- Division of Life Science and RINSGyeongsang National UniversityJinju52828South Korea
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Ramírez-Valiente JA, Solé-Medina A, Robledo-Arnuncio JJ, Ortego J. Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks. Mol Ecol 2023; 32:983-999. [PMID: 36479963 DOI: 10.1111/mec.16816] [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: 08/31/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Improving our knowledge of how past climate-driven selection has acted on present-day trait population divergence is essential to understand local adaptation processes and improve our predictions of evolutionary trajectories in the face of altered selection pressures resulting from climate change. In this study, we investigated signals of selection on traits related to drought tolerance and growth rates in two Mediterranean oak species (Quercus faginea and Q. lusitanica) with contrasting distribution ranges and climatic niches. We genotyped 182 individuals from 24 natural populations of the two species using restriction-site-associated DNA sequencing and conducted a thorough functional characterization in 1602 seedlings from 21 populations cultivated in common garden experiments under contrasting watering treatments. Our genomic data revealed that both Q. faginea and Q. lusitanica have very weak population genetic structure, probably as a result of high rates of pollen-mediated gene flow among populations and large effective population sizes. In contrast, common garden experiments showed evidence of climate-driven divergent selection among populations on traits related to leaf morphology, physiology and growth in both species. Overall, our study suggests that climate is an important selective factor for Mediterranean oaks and that ecophysiological traits have evolved in drought-prone environments even in a context of very high rates of gene flow among populations.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Ecological and Forestry Applications Research Centre, CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
| | - Aida Solé-Medina
- Instituto de Ciencias Forestales (ICIFOR-INIA), CSIC, Madrid, Spain
| | | | - Joaquín Ortego
- Department of Ecology and Evolution, Estación Biológica de Doñana, EBD-CSIC, Seville, Spain
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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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Wu D, Shu M, Moran EV. Heritability of plastic trait changes in drought‐exposed ponderosa pine seedlings. Ecosphere 2023. [DOI: 10.1002/ecs2.4454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Affiliation(s)
- Dean Wu
- School of Natural Sciences University of California Merced Merced California USA
| | - Mengjun Shu
- School of Natural Sciences University of California Merced Merced California USA
| | - Emily V. Moran
- School of Natural Sciences University of California Merced Merced California USA
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Le Provost G, Lalanne C, Lesur I, Louvet JM, Delzon S, Kremer A, Labadie K, Aury JM, Da Silva C, Moritz T, Plomion C. Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology. BMC PLANT BIOLOGY 2023; 23:108. [PMID: 36814198 PMCID: PMC9948485 DOI: 10.1186/s12870-023-04069-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations. RESULTS In the present study, we used an elevation gradient in the Pyrenees Mountains to explore the gene expression network underlying dormancy regulation in natural populations of sessile oak stands sampled along an elevation cline and potentially adapted to different climatic conditions mainly driven by temperature. By performing analyses of gene expression in terminal buds we identified genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Our Results highlighted that low- and high-altitude populations have evolved different molecular strategies for minimizing late frost damage and maximizing the growth period, thereby increasing potentially their respective fitness in these contrasting environmental conditions. More particularly, population from high elevation overexpressed genes involved in the inhibition of cell elongation and delaying flowering time while genes involved in cell division and flowering, enabling buds to flush earlier were identified in population from low elevation. CONCLUSION Our study made it possible to identify key dormancy-by-elevation responsive genes revealing that the stands analyzed in this study have evolved distinct molecular strategies to adapt their bud phenology in response to temperature.
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Affiliation(s)
| | | | - Isabelle Lesur
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- Helix Venture, F-33700, Mérignac, France
| | | | | | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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44
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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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45
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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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46
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Tiret M, Olsson L, Grahn T, Karlsson B, Milesi P, Lascoux M, Lundqvist S, García‐Gil MR. Divergent selection predating the Last Glacial Maximum mainly acted on macro-phenotypes in Norway spruce. Evol Appl 2022; 16:163-172. [PMID: 36699125 PMCID: PMC9850012 DOI: 10.1111/eva.13519] [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: 09/26/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of Q ST vs. F ST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.
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Affiliation(s)
- Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden,Department of Forest Genetics and Plant PhysiologySLU, Umeå Plant Science Centre (UPSC)UmeåSweden,IGEPP, INRAE, Institut Agro, Université de RennesDomaine de la MotteLe RheuFrance
| | | | | | | | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden
| | | | - Maria Rosario García‐Gil
- Department of Forest Genetics and Plant PhysiologySLU, Umeå Plant Science Centre (UPSC)UmeåSweden
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47
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Alía R, Notivol E, Climent J, Pérez F, Barba D, Majada J, García del Barrio JM. Local seed sourcing for sustainable forestry. PLoS One 2022; 17:e0278866. [PMID: 36516142 PMCID: PMC9750025 DOI: 10.1371/journal.pone.0278866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
Seed sourcing strategies are the basis for identifying genetic material meeting the requirements of future climatic conditions and social demands. Specifically, local seed sourcing has been extensively promoted, based on the expected adaptation of the populations to local conditions, but there are some limitations for the application. We analyzed Strict-sense local and Wide-sense local (based on climatic similarity) seed sourcing strategies. We determined species and genetic pools based on these strategies for 40 species and deployment zones in Spain. We also obtained the total number of seed sources and stands for these species in the EU countries. We analyzed the richness of the pools, the relationship with variables related to the use of the species in afforestation, and the availability of seed production areas approved for the production of reproductive material destined to be marketed. This study confirms the existence of extensive species and genetic local pools. Also, that the importance of these pools differs for different species, limitations being derived from the use of forest reproductive material and the existence of approved basic materials. Strategies derived from local seed sourcing approaches are the basis for the use of forest reproductive material because a large number of the species in the area considered in the study are under regulation. However, despite the extensive work done to approve basic materials, limitations based on the availability of seed production areas to provide local material for sustainable forestry are found in those species. Considering a Wide-sense local seed sourcing strategy we provide alternative pools in order to meet social demands under the actual regulations on marketing of reproductive materials.
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Affiliation(s)
- Ricardo Alía
- Department of Ecology and Forest Genetics, Institute of Forest Sciences, INIA-CSIC, Madrid, Spain
- * E-mail:
| | - Eduardo Notivol
- Department of Environment, Agricultural and Forest Systems, CITA, Zaragoza, Spain
| | - José Climent
- Department of Ecology and Forest Genetics, Institute of Forest Sciences, INIA-CSIC, Madrid, Spain
| | - Felipe Pérez
- Directorate General of Biodiversity, Forest and Desertification, MITECO, Madrid, Spain
| | - Diana Barba
- Department of Ecology and Forest Genetics, Institute of Forest Sciences, INIA-CSIC, Madrid, Spain
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48
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Pollution of the Environment and Pollen: A Review. STRESSES 2022. [DOI: 10.3390/stresses2040035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bioindication of the environment is one of the actively developing directions of ecology. Information about pollutants and the level of environmental pollution can be obtained as a result of studying the biological reaction of plants to pollution. Ecological palynology is a new direction, when pollen of various woody and herbaceous species is used for bioindication of the level of environmental pollution and the presence of mutagens. The review considers the morphological variability of pollen, its fertility and viability under the influence of pollutants, the possibility of its use as a bioindicator of pollution of urban areas by emissions of vehicle transport and industry.
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49
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Gorton AJ, Benning JW, Tiffin P, Moeller DA. The spatial scale of adaptation in a native annual plant and its implications for responses to climate change. Evolution 2022; 76:2916-2929. [PMID: 35880454 DOI: 10.1111/evo.14583] [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: 01/22/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 01/22/2023]
Abstract
Spatial patterns of adaptation provide important insights into agents of selection and expected responses of populations to climate change. Robust inference into the spatial scale of adaptation can be gained through reciprocal transplant experiments that combine multiple source populations and common gardens. Here, we examine the spatial scale of local adaptation of the North American annual plant common ragweed, Ambrosia artemisiifolia, using data from four common gardens with 22 source populations sampled from across a ∼1200 km latitudinal gradient within the native range. We found evidence of local adaptation at the northernmost common garden, but maladaptation at the two southern gardens, where more southern source populations outperformed local populations. Overall, the spatial scale of adaptation was large-at the three gardens where distance between source populations and gardens explained variation in fitness, it took an average of 820 km for fitness to decline to 50% of its predicted maximum. Taken together, these results suggest that climate change has already caused maladaptation, especially across the southern portion of the range, and may result in northward range contraction over time.
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Affiliation(s)
- Amanda J Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, 55108
| | - John W Benning
- Department of Botany, University of Wyoming, Laramie, Wyoming, 82071
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108
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50
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Li L, Milesi P, Tiret M, Chen J, Sendrowski J, Baison J, Chen Z, Zhou L, Karlsson B, Berlin M, Westin J, Garcia‐Gil MR, Wu HX, Lascoux M. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. THE NEW PHYTOLOGIST 2022; 236:1976-1987. [PMID: 36093739 PMCID: PMC9828440 DOI: 10.1111/nph.18480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/23/2022] [Indexed: 05/26/2023]
Abstract
Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.
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Affiliation(s)
- Lili Li
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Jun Chen
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
- College of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Janek Sendrowski
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - John Baison
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Zhi‐qiang Chen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Linghua Zhou
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | | | - Mats Berlin
- SkogforskUppsala Science Park751 83UppsalaSweden
| | - Johan Westin
- Unit for Field‐Based Forest ResearchSwedish University of Agricultural SciencesSE‐922 91VindelnSweden
| | - Maria Rosario Garcia‐Gil
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Harry X. Wu
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
- CSIRO National Collection Research AustraliaBlack Mountain LaboratoryCanberraACT2601Australia
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
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