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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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52
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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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53
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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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54
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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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55
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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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56
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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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57
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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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58
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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 2023; 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] [Grants] [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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59
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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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60
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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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61
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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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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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63
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Hopley T, Byrne M. Implications of climate change on a floodplain shrub: associations between genomic and environmental variation. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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64
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Wadgymar SM, DeMarche ML, Josephs EB, Sheth SN, Anderson JT. Local adaptation: Causal agents of selection and adaptive trait divergence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022; 53:87-111. [PMID: 37790997 PMCID: PMC10544833 DOI: 10.1146/annurev-ecolsys-012722-035231] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation.
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Affiliation(s)
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Seema N Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602
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65
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de la Mata R, Zas R, Bustingorri G, Sampedro L, Rust M, Hernandez‐Serrano A, Sala A. Drivers of population differentiation in phenotypic plasticity in a temperate conifer: A 27-year study. Evol Appl 2022; 15:1945-1962. [PMID: 36426125 PMCID: PMC9679231 DOI: 10.1111/eva.13492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
Phenotypic plasticity is a main mechanism for organisms to cope with changing environments and broaden their ecological range. Plasticity is genetically based and can evolve under natural selection, such that populations within a species show distinct phenotypic responses to the environment if evolved under different conditions. Understanding how intraspecific variation in phenotypic plasticity arises is critical to assess potential adaptation to ongoing climate change. Theory predicts that plasticity is favored in more favorable but variable environments. Yet, many theoretical predictions about benefits, costs, and selection on plasticity remain untested. To test these predictions, we took advantage of three genetic trials in the northern Rocky Mountains, USA, which assessed 23 closely located Pinus ponderosa populations over 27 years. Mean environmental conditions and their spatial patterns of variation at the seed source populations were characterized based on six basic climate parameters. Despite the small area of origin, there was significant genetic variation in phenotypic plasticity for tree growth among populations. We found a significant negative correlation between phenotypic plasticity and the patch size of environmental heterogeneity at the seed source populations, but not with total environmental spatial variance. These results show that populations exposed to high microhabitat heterogeneity have evolved higher phenotypic plasticity and that the trigger was the grain rather than the total magnitude of spatial heterogeneity. Contrary to theoretical predictions, we also found a positive relationship between population plasticity and summer drought at the seed source, indicating that drought can act as a trigger of plasticity. Finally, we found a negative correlation between the quantitative genetic variance within populations and their phenotypic plasticity, suggesting compensatory adaptive mechanisms for the lack of genetic diversity. These results improve our understanding of the microevolutionary drivers of phenotypic plasticity, a critical process for resilience of long-lived species under climate change, and support decision-making in tree genetic improvement programs and seed transfer strategies.
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Affiliation(s)
- Raul de la Mata
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
- Estación Biológica de DoñanaConsejo Superior de Investigaciones Científicas (EBD‐CSIC)SevillaSpain
| | - Rafael Zas
- Misión Biológica de GaliciaConsejo Superior de Investigaciones Científicas (MBG‐CSIC)PontevedraSpain
| | - Gloria Bustingorri
- Misión Biológica de GaliciaConsejo Superior de Investigaciones Científicas (MBG‐CSIC)PontevedraSpain
| | - Luis Sampedro
- Misión Biológica de GaliciaConsejo Superior de Investigaciones Científicas (MBG‐CSIC)PontevedraSpain
| | - Marc Rust
- Inland Empire Tree Improvement CooperativeUniversity of IdahoMoscowIdahoUSA
| | - Ana Hernandez‐Serrano
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF)Cerdanyola del VallèsSpain
| | - Anna Sala
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
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66
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Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat Commun 2022; 13:6541. [PMID: 36319648 PMCID: PMC9626627 DOI: 10.1038/s41467-022-34206-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.
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67
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Laport RG, Brookover ZS, Christman BD, Julienne NG, Philley K, Craddock JH. Environmental Niche and Demographic Modeling of American Chestnut near its Southwestern Range Limit. AMERICAN MIDLAND NATURALIST 2022. [DOI: 10.1674/0003-0031-188.2.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | | | - NG Julienne
- Department of Biology, Rhodes College, Memphis, Tennessee 38112
| | - Kevin Philley
- United States Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, Mississippi 39180
| | - J. Hill Craddock
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga 37403
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68
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Ding C, Brouard JS. Assisted migration is plausible for a boreal tree species under climate change: A quantitative and population genetics study of trembling aspen ( Populus tremuloides Michx.) in western Canada. Ecol Evol 2022; 12:e9384. [PMID: 36225831 PMCID: PMC9534759 DOI: 10.1002/ece3.9384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/16/2022] [Indexed: 11/14/2022] Open
Abstract
A novel method was tested for improving tree breeding strategies that integrate quantitative and population genetics based on range-wide reciprocal transplant experiments. Five reciprocal common garden tests of Populus tremuloides were investigated including 6450 trees across western Canada focusing on adaptation traits and growth. Both genetic parameters and home-site transplant models were evaluated. We found a genetic trade-off between growth and early spring leaf flush and late fall senescence. Coefficients of phenotypic variation (CVp) of cell lysis (CL), a measure of freezing injury, shrank from 0.28 to 0.10 during acclimation in the fall, and the CVp slope versus the freezing temperature was significantly different from zero (R 2 = 0.33, p = .02). There was more between-population genetic variation in fall phenology than in spring leaf phenology. We suggest that P. tremuloides demonstrated a discrepancy between the ecological optimum and the physiological optimum minimum winter temperature. The sub-optimal growing condition of P. tremuloides is potentially caused by the warmer ecological optimum than the physiological optimum. Assisted migration and breeding of fast growers to reforest cooler plantation sites can improve productivity. Transferring the study populations to less than 4°C of extreme minimum temperature appears safe for reforestation aligning with the historical recolonization direction of the species. This is equivalent to a 5-10° latitudinal northward movement. Fall frost hardiness is an effective criterion for family selection in the range tested in this study.
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Affiliation(s)
- Chen Ding
- Western Gulf Forest Tree Improvement ProgramTexas A&M Forest Service, TAMU SystemCollege StationTexasUSA
| | - Jean S. Brouard
- Isabella Point Forestry Ltd.Salt Spring IslandBritish ColumbiaCanada
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69
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Liu Y, Erbilgin N, Ratcliffe B, Klutsch JG, Wei X, Ullah A, Cappa EP, Chen C, Thomas BR, El-Kassaby YA. Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations. Proc Biol Sci 2022; 289:20221034. [PMID: 36069017 PMCID: PMC9449467 DOI: 10.1098/rspb.2022.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
While droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e. height growth, drought avoidance based on water-use efficiency inferred from δ13C and pest resistance based on defence traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ13C and increased the evolutionary potential of height growth and δ13C across populations. We found, however, no pronounced gradient in defences and their evolutionary potential along populations or test sites. Response to selection was weak in defences across test sites, but high for height growth particularly at warm test sites. Response to the selection of δ13C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with a limited evolutionary influence from pest (biotic) pressures.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada.,McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK.,Wolfson College, University of Cambridge, Barton Road, Cambridge CB3 9BB, UK
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jennifer G Klutsch
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Xiaojing Wei
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Aziz Ullah
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Eduardo Pablo Cappa
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Recursos Biológicos, Centro de Investigación en Recursos Naturales, De Los Reseros y Doctor Nicolás Repetto s/n, 1686, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Barb R Thomas
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
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70
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Liu M, Liu X, Zhou P, Jiang S, Huang JG, Dong Z. Environmental factors have a major effect in shaping the gene expression of Siberian larch in the Altai Mountains of China. THE PLANT GENOME 2022; 15:e20240. [PMID: 35818680 DOI: 10.1002/tpg2.20240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The differentiation of gene expression is an important link between genotype and phenotype and has important contributions to species adaptation and ecosystem evolution. As a major component of the world's forests, boreal forests play an important role in regulating the global climate, and the phenology of tree species has been and is undergoing changes during global warming. Here, to understand the impact of global warming on gene expression in boreal forest species, we used PacBio and Illumina sequencing methods to study the transcriptome of natural populations of Siberian larch (Larix sibirica Ledeb.) from the Altai Mountains in Xinjiang, China. We found that populations in this area had low genetic differentiation, but individuals were genetically clustered together when they had close geographic distance. Environmental factors, especially temperature, dominated differential gene expression of Siberian larch, while the contribution of genetic variation is relatively small. We speculate that Siberian larch adapts to changes in temperature and precipitation by altering its own gene expression. These results not only predict the tolerance of boreal forests to higher temperatures in the future, but also inform forest management strategies under global climate change.
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Affiliation(s)
- Min Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Univ., Guangzhou, 510006, China
| | - Xiaobin Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Univ., Guangzhou, 510006, China
| | - Peng Zhou
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou, 510650, China
| | - Shaowei Jiang
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou, 510650, China
| | - Jian-Guo Huang
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou, 510650, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Univ., Guangzhou, 510006, China
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71
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Wu X, Wang M, Li X, Yan Y, Dai M, Xie W, Zhou X, Zhang D, Wen Y. Response of distribution patterns of two closely related species in Taxus genus to climate change since last inter-glacial. Ecol Evol 2022; 12:e9302. [PMID: 36177121 PMCID: PMC9475124 DOI: 10.1002/ece3.9302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 02/02/2023] Open
Abstract
Climate change affects the species spatio-temporal distribution deeply. However, how climate affects the spatio-temporal distribution pattern of related species on the large scale remains largely unclear. Here, we selected two closely related species in Taxus genus Taxus chinensis and Taxus mairei to explore their distribution pattern. Four environmental variables were employed to simulate the distribution patterns using the optimized Maxent model. The results showed that the highly suitable area of T. chinensis and T. mairei in current period was 1.616 × 105 km2 and 3.093 × 105 km2, respectively. The distribution area of T. chinensis was smaller than that of T. mairei in different periods. Comparison of different periods shown that the distribution area of the two species was almost in stasis from LIG to the future periods. Temperature and precipitation were the main climate factors that determined the potential distribution of the two species. The centroids of T. chinensis and T. mairei were in Sichuan and Hunan provinces in current period, respectively. In the future, the centroid migration direction of the two species would shift towards northeast. Our results revealed that the average elevation distribution of T. chinensis was higher than that of T. mairei. This study sheds new insights into the habitat preference and limiting environment factors of the two related species and provides a valuable reference for the conservation of these two threatened species.
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Affiliation(s)
- Xingtong Wu
- Central South University of Forestry and TechnologyHunanChina
| | - Minqiu Wang
- Central South University of Forestry and TechnologyHunanChina
| | - Xinyu Li
- Central South University of Forestry and TechnologyHunanChina
| | - Yadan Yan
- Central South University of Forestry and TechnologyHunanChina
| | | | - Wanyu Xie
- Central South University of Forestry and TechnologyHunanChina
| | - Xiaofen Zhou
- Central South University of Forestry and TechnologyHunanChina
| | | | - Yafeng Wen
- Central South University of Forestry and TechnologyHunanChina
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72
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Takahashi M, Goto S, Fukuda Y, Watanabe A. Utility of chloroplast
DNA
haplotype data for ecological restoration using
Fagus crenata
seedlings in case of incomplete seed source information availability. Ecol Res 2022. [DOI: 10.1111/1440-1703.12351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Makoto Takahashi
- Breeding Department, Forest Tree Breeding Center Forestry and Forest Products Research Institute Ibaraki Japan
| | - Susumu Goto
- Education and Research Center, The University of Tokyo Forests Graduate School of Agricultural and Life Sciences, University of Tokyo Bunko‐ku Tokyo Japan
| | - Yoko Fukuda
- Hokkaido Regional Breeding Office, Forest Tree Breeding Center Forestry and Forest Products Research Institute, Midori‐Machi Ebetsu Japan
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73
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Cooper HF, Best RJ, Andrews LV, Corbin JPM, Garthwaite I, Grady KC, Gehring CA, Hultine KR, Whitham TG, Allan GJ. Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species. Mol Ecol 2022; 31:5024-5040. [PMID: 35947510 DOI: 10.1111/mec.16645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST -FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST -FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.
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Affiliation(s)
- Hillary F Cooper
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca J Best
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Lela V Andrews
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Jaclyn P M Corbin
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Iris Garthwaite
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin C Grady
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Catherine A Gehring
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, USA
| | - Thomas G Whitham
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Gerard J Allan
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
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74
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Yu Y, Aitken SN, Rieseberg LH, Wang T. Using landscape genomics to delineate seed and breeding zones for lodgepole pine. THE NEW PHYTOLOGIST 2022; 235:1653-1664. [PMID: 35569109 PMCID: PMC9545436 DOI: 10.1111/nph.18223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Seed and breeding zones traditionally are delineated based on local adaptation of phenotypic traits associated with climate variables, an approach requiring long-term field experiments. In this study, we applied a landscape genomics approach to delineate seed and breeding zones for lodgepole pine. We used a gradient forest (GF) model to select environment-associated single nucleotide polymorphisms (SNPs) using three SNP datasets (full, neutral and candidate) and 20 climate variables for 1906 lodgepole pine (Pinus contorta) individuals in British Columbia and Alberta, Canada. The two GF models built with the full (28 954) and candidate (982) SNPs were compared. The GF models identified winter-related climate as major climatic factors driving genomic patterns of lodgepole pine's local adaptation. Based on the genomic gradients predicted by the full and candidate GF models, lodgepole pine distribution range in British Columbia and Alberta was delineated into six seed and breeding zones. Our approach is a novel and effective alternative to traditional common garden approaches for delineating seed and breeding zone, and could be applied to tree species lacking data from provenance trials or common garden experiments.
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Affiliation(s)
- Yue Yu
- Department of Forest Sciences, Centre for Forest Conservation GeneticsUniversity of British Columbia3041‐2424 Main MallVancouverBCV6T 1Z4Canada
| | - Sally N. Aitken
- Department of Forest Sciences, Centre for Forest Conservation GeneticsUniversity of British Columbia3041‐2424 Main MallVancouverBCV6T 1Z4Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British Columbia6270 University BoulevardVancouverBCV6T 1Z4Canada
| | - Tongli Wang
- Department of Forest Sciences, Centre for Forest Conservation GeneticsUniversity of British Columbia3041‐2424 Main MallVancouverBCV6T 1Z4Canada
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75
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Climate Change in the Provenance Regions of Romania over the Last 70 Years: Implications for Forest Management. FORESTS 2022. [DOI: 10.3390/f13081203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The recent climate change scenarios show significant increases in temperature and extreme drought events in Southern and Eastern Europe by the end of the 21st century, which will have a serious impact on forest growth and adaptation, and important consequences for forest management. The system of provenance regions, according to the OECD Scheme and EU Directive, was thought to encourage the use of the local seed sources, under the concept ‘local is the best’. However, climate is changing faster than some species or populations can adapt or migrate, which raises some uncertainties with respect to the future performance of local populations. In Romania, as in other countries, the delimitation of provenance regions is based on geographical, ecological and vegetation criteria. The aim of this study is to evaluate: (1) the climate change that has occurred at the level of the provenance regions; (2) which regions will be most vulnerable to climate change; (3) which forest types will be the most vulnerable in a certain region; and (4) changes in the climatic envelope of forest species. Several climatic parameters and an ecoclimatic indices have been calculated and analyzed at the level of provenance regions, subregions and ecological sectors (forest types) in Romania, during the period 1951–2020. The results highlight a general shift towards warmer and drier conditions in the last 30 years, the mean annual temperature increasing with 0.3–1.1 °C across the provenance subregions. The De Martonne aridity index for the vegetation season shows that 86% of the ecological sectors fell into the arid and semiarid categories, which indicates a very high degree of vulnerability for forest species. On the Lang rainfall index, forest steppe climatic conditions occurred in all pure or mixed pedunculate oak forests, thermophile oak species, meadow forests, poplar and willow, Turkey oak and Hungarian oak forests. The Ellenberg coefficient highlights that the warming process is more evident along the altitude and the degree of vulnerability increase at lower altitude or at the edge of species distribution. The climate envelopes of many forest species have already shifted to another ecosystem’s climate. This paper presents the importance of re-delineation the provenance regions for the production and deployment of forest reproductive materials according to the climate change occurred in the last decades, as a fundamental tool for an adaptive forest management.
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76
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Sandercock AM, Westbrook JW, Zhang Q, Johnson HA, Saielli TM, Scrivani JA, Fitzsimmons SF, Collins K, Perkins MT, Craddock JH, Schmutz J, Grimwood J, Holliday JA. Frozen in time: rangewide genomic diversity, structure, and demographic history of relict American chestnut populations. Mol Ecol 2022; 31:4640-4655. [PMID: 35880415 DOI: 10.1111/mec.16629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Abstract
American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the eastern United States. In the first half of the 20th century, an exotic fungal pathogen - Cryphonectria parasitica - decimated the species, killing billions of chestnut trees. Two approaches to developing blight resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted restoration populations. Here we characterize population structure, demographic history, and genomic diversity in a range-wide sample of 384 wild American chestnuts to inform conservation and breeding with blight resistant varieties. Population structure analyses suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within-population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defense against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant genetic populations. These populations will serve as management units for breeding adaptive genetic variation into the blight-resistant tree populations for targeted reintroduction efforts.
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Affiliation(s)
| | | | - Qian Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Hayley A Johnson
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | | | | | | | | | - M Taylor Perkins
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - J Hill Craddock
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
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77
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Martínez de León R, Castellanos-Morales G, Moreno-Letelier A. Incipient speciation, high genetic diversity, and ecological divergence in the alligator bark juniper suggest complex demographic changes during the Pleistocene. PeerJ 2022; 10:e13802. [PMID: 35910768 PMCID: PMC9336613 DOI: 10.7717/peerj.13802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
The most recent glacial cycles of the Pleistocene affected the distribution, population sizes, and levels of genetic structure of temperate-forest species in the main Mexican mountain systems. Our objective was to investigate the effects these cycles had on the genetic structure and distribution of a dominant species of the "mexical" vegetation across North and Central America. We studied the genetic diversity of Juniperus deppeana, a conifer distributed from the Southwestern United States to the highlands of Central America. We combined information of one plastid marker and two nuclear markers to infer phylogeographic structure, genetic diversity and demographic changes. We also characterized the climatic niche for each variety to infer the plausible area of suitability during past climatic conditions and to evaluate climatic niche discontinuities along with the species distribution. We found a marked phylogeographic structure separating the populations North and South of the Isthmus of Tehuantepec, with populations to the South of this barrier forming a distinct genetic cluster corresponding to Juniperus deppeana var. gamboana. We also found signals of population expansion in the Northern genetic cluster. Ecological niche modeling results confirmed climatic niche differences and discontinuities among J. deppeana varieties and heterogeneous responses to climatic oscillations. Overall, J. deppeana's genetic diversity has been marked by distribution shifts, population growth and secondary contact the North, and in situ permanence in the South since the last interglacial to the present. High genetic variation suggests a wide and climatically diverse distribution during climatic oscillations. We detected the existence of two main genetic clusters, supporting previous proposals that Juniperus deppeana and Juniperus gamboana may be considered two separate species.
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Affiliation(s)
- Rodrigo Martínez de León
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico,Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Alejandra Moreno-Letelier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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78
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Du S, Hu X, Yang X, Yu W, Wang Z. Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China. Ecol Evol 2022; 12:e9101. [PMID: 35898427 PMCID: PMC9309028 DOI: 10.1002/ece3.9101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/04/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.
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Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern ChinaShanxi Agricultural University TaiguJinzhongChina
| | - Xiaoyan Hu
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern ChinaShanxi Agricultural University TaiguJinzhongChina
| | - Xiuyun Yang
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern ChinaShanxi Agricultural University TaiguJinzhongChina
| | - Wendong Yu
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouChina
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
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79
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Sousa F, Costa J, Ribeiro C, Varandas M, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel C, Veloso MM, Oliveira M, Pinto Ricardo C, Batista D, Paulo OS. Population structure in Quercus suber L. revealed by nuclear microsatellite markers. PeerJ 2022; 10:e13565. [PMID: 35729909 PMCID: PMC9206845 DOI: 10.7717/peerj.13565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure.
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Affiliation(s)
- Filipe Sousa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Joana Costa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,RAIZ, Herdade de Espirra, Pegões, Portugal
| | - Carla Ribeiro
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Marta Varandas
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Francisco Pina-Martins
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Polytechnic Institute of Setúbal, ESTBarreiro, Setúbal, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - José Matos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Maria Glushkova
- Forest Research Institute of B.A.S., Department of Forest Genetics, Physiology and Plantations, Sofia, Bulgaria
| | - Célia Miguel
- Faculdade de Ciências, Universidade de Lisboa, Biosystems & Integrative Sciences Institute, Lisboa, Portugal,iBET, Oeiras, Portugal
| | - Maria Manuela Veloso
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Margarida Oliveira
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cândido Pinto Ricardo
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Dora Batista
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Instituto Superior de Agronomia, Universidade de Lisboa, LEAF—Linking Landscape, Environment, Agriculture and Food (LEAF), Lisboa, Portugal
| | - Octávio S. Paulo
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
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80
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St.Clair JB, Richardson BA, Stevenson‐Molnar N, Howe GT, Bower AD, Erickson VJ, Ward B, Bachelet D, Kilkenny FF, Wang T. Seedlot Selection Tool and Climate‐Smart Restoration Tool: Web‐based tools for sourcing seed adapted to future climates. Ecosphere 2022. [DOI: 10.1002/ecs2.4089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | | | | | - Glenn T. Howe
- Department of Forest Ecosystems and Society Oregon State University Corvallis Oregon USA
| | - Andrew D. Bower
- Olympic National Forest USDA‐Forest Service Olympia Washington USA
| | | | - Brendan Ward
- Conservation Biology Institute Corvallis Oregon USA
| | | | | | - Tongli Wang
- Centre for Forest Conservation Genetics, Department of Forest and Conservation Science University of British Columbia Vancouver British Columbia Canada
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81
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Orsucci M, Yang X, Vanikiotis T, Guerrina M, Duan T, Lascoux M, Glémin S. Competitive ability depends on mating system and ploidy level across Capsella species. ANNALS OF BOTANY 2022; 129:697-708. [PMID: 35325927 PMCID: PMC9113120 DOI: 10.1093/aob/mcac044] [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: 12/22/2021] [Revised: 10/14/2021] [Accepted: 03/23/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy, and selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers and, within selfers, in polyploids than in diploids. Although often proposed in the botanical literature and also suggested by meta-analyses, these predictions have not been directly tested yet. METHODS In order to compare fitness and the competitive ability of four Capsella species with a different mating system and ploidy level, we combined two complementary experiments. First, we carried out an experiment outdoors in north-west Greece, i.e. within the range of the obligate outcrossing species, C. grandiflora, where several life history traits were measured under two different disturbance treatments, weeded plots vs. unweeded plots. To better control competition and to remove potential effects of local adaptation of the outcrosser, we also performed a similar competition experiment but under growth chamber conditions. KEY RESULTS In the outdoor experiment, disturbance of the environment did not affect the phenotype in any of the four species. For most traits, the obligate outcrossing species performed better than all selfing species. In contrast, polyploids did not survive or reproduce better than diploids. Under controlled conditions, as in the field experiment, the outcrosser had a higher fitness than selfing species and was less affected by competition. Finally, contrary to the outdoor experiment where the two behaved identically, polyploid selfers were less affected by competition than diploid selfes. CONCLUSIONS In the Capsella genus, selfing induces lower fitness than outcrossing and can also reduce competitive ability. The effect of polyploidy is, however, unclear. These results highlight the possible roles of ecological context in the evolution of selfing species.
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Affiliation(s)
- Marion Orsucci
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Xuyue Yang
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Theofilos Vanikiotis
- Department of Biological Applications & Technology, University of Ioannina, Leof. S. Niarchou GR-451 10, Ioannina, Greece
| | - Maria Guerrina
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
- UMR CNRS 6553 ECOBIO, Campus Beaulieu, bât 14a, CS 74205, 35042 Rennes, France
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82
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Tsumura Y. Genetic structure and local adaptation in natural forests of
Cryptomeria japonica
. Ecol Res 2022. [DOI: 10.1111/1440-1703.12320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba Ibaraki Japan
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83
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Evidence for continent-wide convergent evolution and stasis throughout 150 y of a biological invasion. Proc Natl Acad Sci U S A 2022; 119:e2107584119. [PMID: 35476511 PMCID: PMC9170017 DOI: 10.1073/pnas.2107584119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adaptive evolution can help species to persist and spread in new environments, but it is unclear how the rate and duration of adaptive evolution vary throughout species ranges and on the decadal timescales most relevant to managing biodiversity for the 21st century. Using herbarium records, we reconstruct 150 y of evolution in an invasive plant as it spread across North America. Flowering phenology evolves to adapt to local growing seasons throughout the range but stalls after about a century. This punctuated, convergent evolution recapitulates long-term dynamics in the fossil record, implicating limits to evolutionary rates that are not evident for the first century of spread. The extent to which evolution can rescue a species from extinction, or facilitate range expansion, depends critically on the rate, duration, and geographical extent of the evolutionary response to natural selection. Adaptive evolution can occur quickly, but the duration and geographical extent of contemporary evolution in natural systems remain poorly studied. This is particularly true for species with large geographical ranges and for timescales that lie between “long-term” field experiments and the fossil record. Here, we introduce the Virtual Common Garden (VCG) to investigate phenotypic evolution in natural history collections while controlling for phenotypic plasticity in response to local growing conditions. Reconstructing 150 y of evolution in Lythrum salicaria (purple loosestrife) as it invaded North America, we analyze phenology measurements of 3,429 herbarium records, reconstruct growing conditions from more than 12 million local temperature records, and validate predictions across three common gardens spanning 10° of latitude. We find that phenological clines have evolved repeatedly throughout the range, during the first century of evolution. Thereafter, the rate of microevolution stalls, recapitulating macroevolutionary stasis observed in the fossil record. Our study demonstrates that preserved specimens are a critical resource for investigating limits to evolution in natural populations. Our results show how natural selection and trade-offs measured in field studies predict adaptive divergence observable in herbarium specimens over 15 decades at a continental scale.
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84
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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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85
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Prakash A, DeYoung S, Lachmuth S, Adams JL, Johnsen K, Butnor JR, Nelson DM, Fitzpatrick MC, Keller SR. Genotypic variation and plasticity in climate-adaptive traits after range expansion and fragmentation of red spruce ( Picea rubens Sarg.). Philos Trans R Soc Lond B Biol Sci 2022; 377:20210008. [PMID: 35184589 PMCID: PMC8859516 DOI: 10.1098/rstb.2021.0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/10/2022] [Indexed: 01/18/2023] Open
Abstract
Shifting range limits are predicted for many species as the climate warms. However, the rapid pace of climate change will challenge the natural dispersal capacity of long-lived, sessile organisms such as forest trees. Adaptive responses of populations will, therefore, depend on levels of genetic variation and plasticity for climate-responsive traits, which likely vary across the range due to expansion history and current patterns of selection. Here, we study levels of genetic and plastic variation for phenology and growth traits in populations of red spruce (Picea rubens), from the range core to the highly fragmented trailing edge. We measured more than 5000 offspring sampled from three genetically distinct regions (core, margin and edge) grown in three common gardens replicated along a latitudinal gradient. Genetic variation in phenology and growth showed low to moderate heritability and differentiation among regions, suggesting some potential to respond to selection. Phenology traits were highly plastic, but this plasticity was generally neutral or maladaptive in the effect on growth, revealing a potential liability under warmer climates. These results suggest future climate adaptation will depend on the regional availability of genetic variation in red spruce and provide a resource for the design and management of assisted gene flow. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.
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Affiliation(s)
- Anoob Prakash
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
| | - Sonia DeYoung
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
| | - Susanne Lachmuth
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Jacquelyne L. Adams
- Bent Creek Experimental Forest, USDA Forest Service, Asheville, NC 28806, USA
| | - Kurt Johnsen
- Bent Creek Experimental Forest, USDA Forest Service, Asheville, NC 28806, USA
| | - John R. Butnor
- USDA Forest Service, Southern Research Station, University of Vermont, Burlington, VT 05405, USA
| | - David M. Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
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86
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Wijethunga U, Greenlees M, Elphick M, Shine R. No evidence for cold-adapted life-history traits in cool-climate populations of invasive cane toads (Rhinella marina). PLoS One 2022; 17:e0266708. [PMID: 35390099 PMCID: PMC8989335 DOI: 10.1371/journal.pone.0266708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
As an invasive organism spreads into a novel environment, it may encounter strong selective pressures to adapt to abiotic and biotic challenges. We examined the effect of water temperature during larval life on rates of survival and growth of the early life-history stages of cane toads (Rhinella marina) from two geographic regions (tropical vs. temperate) in the species’ invaded range in eastern Australia. If local adaptation at the southern (cool-climate) invasion front has extended the cold-tolerance of early life-stages, we would expect to see higher viability of southern-population toads under cooler conditions. Our comparisons revealed no such divergence: the effects of water temperature on rates of larval survival and growth, time to metamorphosis, size at metamorphosis and locomotor performance of metamorphs were similar in both sets of populations. In two cases where tropical and temperate-zone populations diverged in responses to temperature, the tropical animals performed better at low to medium temperatures than did conspecifics from cooler regions. Adaptation to low temperatures in the south might be constrained by behavioural shifts (e.g., in reproductive seasonality, spawning-site selection) that allow toads to breed in warmer water even in cool climates, by gene flow from warmer-climate populations, or by phylogenetic conservatism in these traits.
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Affiliation(s)
- Uditha Wijethunga
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Matthew Greenlees
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Melanie Elphick
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail:
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87
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Crous KY, Uddling J, De Kauwe MG. Temperature responses of photosynthesis and respiration in evergreen trees from boreal to tropical latitudes. THE NEW PHYTOLOGIST 2022; 234:353-374. [PMID: 35007351 PMCID: PMC9994441 DOI: 10.1111/nph.17951] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/03/2021] [Indexed: 05/29/2023]
Abstract
Evergreen species are widespread across the globe, representing two major plant functional forms in terrestrial models. We reviewed and analysed the responses of photosynthesis and respiration to warming in 101 evergreen species from boreal to tropical biomes. Summertime temperatures affected both latitudinal gas exchange rates and the degree of responsiveness to experimental warming. The decrease in net photosynthesis at 25°C (Anet25 ) was larger with warming in tropical climates than cooler ones. Respiration at 25°C (R25 ) was reduced by 14% in response to warming across species and biomes. Gymnosperms were more sensitive to greater amounts of warming than broadleaved evergreens, with Anet25 and R25 reduced c. 30-40% with > 10°C warming. While standardised rates of carboxylation (Vcmax25 ) and electron transport (Jmax25 ) adjusted to warming, the magnitude of this adjustment was not related to warming amount (range 0.6-16°C). The temperature optimum of photosynthesis (ToptA ) increased on average 0.34°C per °C warming. The combination of more constrained acclimation of photosynthesis and increasing respiration rates with warming could possibly result in a reduced carbon sink in future warmer climates. The predictable patterns of thermal acclimation across biomes provide a strong basis to improve modelling predictions of the future terrestrial carbon sink with warming.
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Affiliation(s)
- Kristine Y. Crous
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797PenrithNSW2751Australia
| | - Johan Uddling
- Department of Biological and Environmental SciencesUniversity of GothenburgPO Box 461GothenburgSE‐405 30Sweden
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88
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Population Differentiation in Acer platanoides L. at the Regional Scale—Laying the Basis for Effective Conservation of Its Genetic Resources in Austria. FORESTS 2022. [DOI: 10.3390/f13040552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Norway maple (Acer platanoides L.) is a widespread forest tree species in Central and Northern Europe but with a scattered distribution. In the debate on climate change driven changes in species selection in the forest, Norway maple has recently received raised interest because of its comparatively high drought resistance (higher than in sycamore maple). Therefore, it is an interesting species for sites high in carbonates and where other native tree species have become devastated by pathogens (e.g., elm, ash). In Austria, the demand on saplings is currently rising, while there is only very little domestic reproductive material available (on average more than 95% of saplings are imported from neighboring countries). This study was undertaken to identify genetic diversity and population structure of Norway maple in Austria to lay the foundation for the establishment of respective in situ and ex situ conservation measures. In addition, samples from planted stands and imported reproductive material from other countries were included to study the anthropogenic influence on the species in managed forests. We used 11 novel microsatellites to genotype 756 samples from 27 putatively natural Austrian populations, and 186 samples derived from two planted stands and five lots of forest reproductive material; in addition, 106 samples from other European populations were also genotyped. Cross species amplification of the new markers was tested in 19 Acer species from around the world. Population clustering by STRUCTURE analysis revealed a distinct pattern of population structure in Austria and Europe, but overall moderate differentiation. Sibship analysis identifies several populations with severe founding effects, highlighting the need for proper selection of seed sources of sufficient genetic diversity in the species.
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89
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de Deus Vidal Junior J, Mori GM, Cruz MV, da Silva MF, de Moura YA, de Souza AP. Differential Adaptive Potential and Vulnerability to Climate-Driven Habitat Loss in Brazilian Mangroves. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.763325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Geographic and environmental differences have been identified as factors influencing Brazilian mangrove trees' genetic diversity. Geographically, distinct species have convergent spatial genetic structures, indicating a limited gene flow between northern and southern populations. Environmentally, genomic studies and common garden experiments have found evidence of local adaptations along the latitudinal gradient of the Brazilian coast. However, little is known about how such adaptive heterogeneity could be affected by a rapidly changing climate in the coming decades, and the combination of deforestation and climate-induced habitat loss may affect these forests and their genetic diversity. Here, we applied two genomic-environmental association methods to model the turnover of potentially adaptive alleles for two dominant mangrove trees: Avicennia germinans and A. schaueriana. We analyzed a total of 134 individuals from six populations of A. germinans and 10 populations of A. schaueriana spanning the Brazilian coast from 1 °S to 28 °S. Gradient forest models identified temperature-related variables as the most important predictors for A. germinans outlier loci, whereas both temperature and precipitation were important for A. schaueriana. We modeled allele frequencies and projected them for future climatic scenarios to estimate adaptively driven vulnerability. We assessed climate-driven habitat loss through climate-only distribution models and calculated annual deforestation rates for each sampled region. Finally, to assess the vulnerability of individual populations, we combined the environmental suitability, deforestation data, and adaptive vulnerability projections. For both species, subtropical populations presented a higher vulnerability than equatorial populations to climate-driven habitat loss. We also identified deforestation rates at the sampled sites that were alarmingly higher than the global average mangrove deforestation rate. Our results provide improved estimates of the impacts of ongoing climate change and human-caused habitat loss on the distribution of mangroves and highlight the importance of site-based conservation strategies that consider individual subtropical and equatorial mangrove forests.
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90
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de Miguel M, Rodríguez-Quilón I, Heuertz M, Hurel A, Grivet D, Jaramillo-Correa JP, Vendramin GG, Plomion C, Majada J, Alía R, Eckert AJ, González-Martínez SC. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Mol Ecol 2022; 31:2089-2105. [PMID: 35075727 DOI: 10.1111/mec.16367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic, i.e., they have a genetic architecture determined by numerous loci each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response traits) in a clonal common-garden network, planted in contrasted environments (over 12,500 trees). Most of the analyzed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change.
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Affiliation(s)
- 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
| | - Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Agathe Hurel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Juan-Pablo Jaramillo-Correa
- Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México City, CDMX 04510, Mexico
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino (FI), Italy
| | | | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental ''La Mata'', 33820, Grado, Principado de Asturias, Spain
| | - Ricardo Alía
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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91
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Ma T, Parker T, Unger S, Gewirtzman J, Fetcher N, Moody ML, Tang J. Responses of root phenology in ecotypes of Eriophorum vaginatum to transplantation and warming in the Arctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149926. [PMID: 34543789 DOI: 10.1016/j.scitotenv.2021.149926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 07/15/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
The effect of climate change on phenology and growth is less understood for belowground plant tissues than for aboveground plant tissues, particularly in high-latitude regions. Ecotypes within a species adapted to a locality may display different responses to climate change. We established two common garden plots in the Arctic tundra north of the Brooks Range in northern Alaska. Three ecotypes of Eriophorum vaginatum along a latitudinal gradient were transplanted into common gardens, and half of the transplants were warmed using open-top chambers (OTCs). Minirhizotrons were used to track the root phenology during the growing seasons of 2016 and 2017. Warming with OTCs (approximately +1 °C in air) did not affect the root biomass, root production or root phenology. The southern ecotype (from 67°16'N) of Eriophorum vaginatum transplanted northward experienced delayed startup and root production compared to two northern ecotypes (from 68°38'N and 69°25'N), although significant differences were not observed in the three ecotypes in terms of root production, root biomass and growth duration at the two sites. Our results suggest that as the climate warms, ecotypes of Eriophorum vaginatum may be able to adjust their duration of root growth and root productivity by phenotypic plasticity, although the degree of plasticity controlling the root startup time may vary between southern and northern ecotypes.
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Affiliation(s)
- Ting Ma
- The Ecosystems Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543, USA; Lanzhou University, Lanzhou, China.
| | - Thomas Parker
- The Ecosystems Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543, USA; Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Steven Unger
- The Ecosystems Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543, USA
| | | | - Ned Fetcher
- Institute for Environmental Science and Sustainability, Wilkes University, Wilkes-Barre, PA, USA
| | - Michael L Moody
- Biological Sciences, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Jianwu Tang
- The Ecosystems Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543, USA.
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92
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Hu Y, Feng C, Yang L, Edger PP, Kang M. Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis. HORTICULTURE RESEARCH 2022; 9:uhab059. [PMID: 35043184 PMCID: PMC8993681 DOI: 10.1093/hr/uhab059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
The crop wild relative, Fragaria nilgerrensis, is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve useful to guide the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and the genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibited the highest genetic diversity. Redundancy analysis suggests that both environment and geographic variables shaped a significant proportion of genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweeps scans and genome-environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis.
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Affiliation(s)
- Yuxi Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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93
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Kudryavtsev AY, Oparin ML, Oparina OS, Mamaev AB, Kovalev DV. State of Birch Outliers in the Southern Trans-Urals in the Zone of High Anthropogenic Load on Natural Ecosystems. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021100186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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94
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Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient. Sci Rep 2021; 11:24333. [PMID: 34934087 PMCID: PMC8692458 DOI: 10.1038/s41598-021-03548-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Immortelle (Helichrysum italicum (Roth) G. Don; Asteraceae) is a perennial plant species native to the Mediterranean region, known for many properties with wide application mainly in perfume and cosmetic industry. A total of 18 wild H. italicum populations systematically sampled along the eastern Adriatic environmental gradient were studied using AFLP markers to determine genetic diversity and structure and to identify loci potentially responsible for adaptive divergence. Results showed higher levels of intrapopulation diversity than interpopulation diversity. Genetic differentiation among populations was significant but low, indicating extensive gene flow between populations. Bayesian analysis of population structure revealed the existence of two genetic clusters. Combining the results of FST - outlier analysis (Mcheza and BayeScan) and genome-environment association analysis (Samβada, LFMM) four AFLP loci strongly associated with the bioclimatic variables Bio03 Isothermality, Bio08 Mean temperature of the wettest quarter, Bio15 Precipitation seasonality, and Bio17 Precipitation of driest quarter were found to be the main variables driving potential adaptive genetic variation in H. italicum along the eastern Adriatic environmental gradient. Redundancy analysis revealed that the partitioning of genetic variation was mainly associated with the adaptation to temperature oscillations. The results of the research may contribute to a clearer understanding of the importance of local adaptations for the genetic differentiation of Mediterranean plants and allow the planning of appropriate conservation strategies. However, considering that the identified outlier loci may be linked to genes under selection rather than being the target of natural selection, future studies must aim at their additional analysis.
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95
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Chen Y, Liu Z, Régnière J, Vasseur L, Lin J, Huang S, Ke F, Chen S, Li J, Huang J, Gurr GM, You M, You S. Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest. Nat Commun 2021; 12:7206. [PMID: 34893609 PMCID: PMC8664911 DOI: 10.1038/s41467-021-27510-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/22/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding the genetic basis of climatic adaptation is essential for predicting species' responses to climate change. However, intraspecific variation of these responses arising from local adaptation remains ambiguous for most species. Here, we analyze genomic data from diamondback moth (Plutella xylostella) collected from 75 sites spanning six continents to reveal that climate-associated adaptive variation exhibits a roughly latitudinal pattern. By developing an eco-genetic index that combines genetic variation and physiological responses, we predict that most P. xylostella populations have high tolerance to projected future climates. Using genome editing, a key gene, PxCad, emerged from our analysis as functionally temperature responsive. Our results demonstrate that P. xylostella is largely capable of tolerating future climates in most of the world and will remain a global pest beyond 2050. This work improves our understanding of adaptive variation along environmental gradients, and advances pest forecasting by highlighting the genetic basis for local climate adaptation.
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Affiliation(s)
- Yanting Chen
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.418033.d0000 0001 2229 4212Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 China
| | - Zhaoxia Liu
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.449406.b0000 0004 1757 7252College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, 362000 China
| | - Jacques Régnière
- grid.146611.50000 0001 0775 5922Natural Resources Canada, Canadian Forest Service, Quebec City, QC G1V 4C7 Canada
| | - Liette Vasseur
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,grid.411793.90000 0004 1936 9318Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1 Canada
| | - Jian Lin
- grid.256111.00000 0004 1760 2876College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiguo Huang
- grid.256111.00000 0004 1760 2876College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Fushi Ke
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Shaoping Chen
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.418033.d0000 0001 2229 4212Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 China
| | - Jianyu Li
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China ,grid.418033.d0000 0001 2229 4212Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 China
| | - Jieling Huang
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002 China
| | - Geoff M. Gurr
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.419897.a0000 0004 0369 313XJoint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002 China ,grid.1037.50000 0004 0368 0777Graham Centre, Charles Sturt University, Orange, NSW 2800 Australia
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China. .,Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
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96
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Ascoli D, Hacket-Pain A, Pearse IS, Vacchiano G, Corti S, Davini P. Modes of climate variability bridge proximate and evolutionary mechanisms of masting. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200380. [PMID: 34657463 PMCID: PMC8520781 DOI: 10.1098/rstb.2020.0380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 11/12/2022] Open
Abstract
There is evidence that variable and synchronous reproduction in seed plants (masting) correlates to modes of climate variability, e.g. El Niño Southern Oscillation and North Atlantic Oscillation. In this perspective, we explore the breadth of knowledge on how climate modes control reproduction in major masting species throughout Earth's biomes. We posit that intrinsic properties of climate modes (periodicity, persistence and trends) drive interannual and decadal variability of plant reproduction, as well as the spatial extent of its synchrony, aligning multiple proximate causes of masting through space and time. Moreover, climate modes force lagged but in-phase ecological processes that interact synergistically with multiple stages of plant reproductive cycles. This sets up adaptive benefits by increasing offspring fitness through either economies of scale or environmental prediction. Community-wide links between climate modes and masting across plant taxa suggest an evolutionary role of climate variability. We argue that climate modes may 'bridge' proximate and ultimate causes of masting selecting for variable and synchronous reproduction. The future of such interaction is uncertain: processes that improve reproductive fitness may remain coupled with climate modes even under changing climates, but chances are that abrupt global warming will affect Earth's climate modes so rapidly as to alter ecological and evolutionary links. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.
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Affiliation(s)
- Davide Ascoli
- Department DISAFA, University of Torino (IT), Torino TO, Italy
| | - Andrew Hacket-Pain
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool (UK), UK
| | - Ian S. Pearse
- Fort Collins Science Center, US Geological Survey, Fort Collins, CO, USA
| | | | - Susanna Corti
- Istituto di Scienze dell'Atmosfera e del Clima, Consiglio Nazionale delle Ricerche (CNR-ISAC), Bologna, Italy
| | - Paolo Davini
- Istituto di Scienze dell'Atmosfera e del Clima, Consiglio Nazionale delle Ricerche (CNR-ISAC), Torino, Italy
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97
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Hurel A, de Miguel M, Dutech C, Desprez‐Loustau M, Plomion C, Rodríguez‐Quilón I, Cyrille A, Guzman T, Alía R, González‐Martínez SC, Budde KB. Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine. Evol Appl 2021; 14:2750-2772. [PMID: 34950227 PMCID: PMC8674897 DOI: 10.1111/eva.13309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/03/2021] [Indexed: 11/30/2022] Open
Abstract
Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), spring phenology (0.165-0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome-wide SNPs revealed several loci significantly associated with each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
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Affiliation(s)
- Agathe Hurel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | - Marina de Miguel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- EGFV, INRAEUniversity of BordeauxVillenave‐d'OrnonFrance
| | - Cyril Dutech
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | | | | | | | | | | | | | | | - Katharina B. Budde
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- Büsgen‐InstituteGeorg‐August University GöttingenGöttingenGermany
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98
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Genetic diversity of Norway spruce ecotypes assessed by GBS-derived SNPs. Sci Rep 2021; 11:23119. [PMID: 34848793 PMCID: PMC8632914 DOI: 10.1038/s41598-021-02545-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/11/2021] [Indexed: 11/08/2022] Open
Abstract
We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low- (acuminata), medium- (europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRUCTURE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.
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99
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Poupon V, Chakraborty D, Stejskal J, Konrad H, Schueler S, Lstibůrek M. Accelerating Adaptation of Forest Trees to Climate Change Using Individual Tree Response Functions. FRONTIERS IN PLANT SCIENCE 2021; 12:758221. [PMID: 34887888 PMCID: PMC8650053 DOI: 10.3389/fpls.2021.758221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
In forest tree breeding, assisted migration has been proposed to accelerate the adaptive response to climate change. Response functions are currently fitted across multiple populations and environments, enabling selections of the most appropriate seed sources for a specific reforestation site. So far, the approach has been limited to capturing adaptive variation among populations, neglecting tree-to-tree variation residing within a population. Here, we combined the response function methodology with the in-situ breeding approach, utilizing progeny trials of European larch (Larix decidua) across 21 test sites in Austria ranging from Alpine to lowland regions. We quantified intra-population genetic variance and predicted individual genetic performance along a climatic gradient. This approach can be adopted in most breeding and conservation programs, boosting the speed of adaptation under climate change.
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Affiliation(s)
- Valérie Poupon
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
| | - Debojyoti Chakraborty
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape, Department of Forest Growth, Silviculture & Genetics, Vienna, Austria
| | - Jan Stejskal
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
| | - Heino Konrad
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape, Department of Forest Biodiversity and Nature Conservation, Vienna, Austria
| | - Silvio Schueler
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape, Department of Forest Growth, Silviculture & Genetics, Vienna, Austria
| | - Milan Lstibůrek
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
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100
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Growth Recovery and Phenological Responses of Juvenile Beech (Fagus sylvatica L.) Exposed to Spring Warming and Late Spring Frost. FORESTS 2021. [DOI: 10.3390/f12111604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Global change increases the risk of extreme climatic events. The impact of extreme temperature may depend on the tree species and also on the provenance. Ten provenances of Fagus sylvatica L. were grown in a common garden environment in Belgium and subjected to different temperature treatments. Half of the one year old seedlings were submitted to a high thermal stress in the spring of the first year, and all plants were exposed to a late spring frost in the second year. The high-temperature treated plants displayed reduced growth in the first year, which was fully compensated (recovery with exact compensation) in the second year for radial growth and in the third year for height growth. Frost in the spring of the second year damaged part of the saplings and reduced their growth. The frost damaged plants regained the pre-stress growth rate one year later (recovery without compensation). The high temperature treatment in the first year and the frost damage in the second year clearly influenced the phenological responses in the year of the event and in the succeeding year. Little population differentiation was observed among the provenances for growth and for phenological responses. Yet, a southern provenance, a non-autochthonous provenance (original German provenance that was planted in Belgium about a century ago) and a more continental provenance flushed earlier than the local Atlantic provenances in the year of the frost event, resulting in more frost damage. Some caution should therefore be taken when translocating provenances as an anticipation of the predicted climate warming.
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