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Guillaume AS, Leempoel K, Rogivue A, Gugerli F, Parisod C, Joost S. Integrating very high resolution environmental proxies in genotype-environment association studies. Evol Appl 2024; 17:e13737. [PMID: 38948540 PMCID: PMC11212006 DOI: 10.1111/eva.13737] [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: 06/02/2023] [Revised: 02/20/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype-environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant Arabis alpina L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.
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Affiliation(s)
- Annie S. Guillaume
- Geospatial Molecular Epidemiology Group (GEOME), Laboratory for Biological Geochemistry (LGB), Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Kevin Leempoel
- Geospatial Molecular Epidemiology Group (GEOME), Laboratory for Biological Geochemistry (LGB), Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Royal Botanic Gardens, KewRichmond, SurreyUK
| | - Aude Rogivue
- WSL Swiss Federal Research InstituteBirmensdorfSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research InstituteBirmensdorfSwitzerland
| | | | - Stéphane Joost
- Geospatial Molecular Epidemiology Group (GEOME), Laboratory for Biological Geochemistry (LGB), Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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Aitken SN, Jordan R, Tumas HR. Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:707-736. [PMID: 38594931 DOI: 10.1146/annurev-arplant-070523-044239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.
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Affiliation(s)
- Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| | | | - Hayley R Tumas
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
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3
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Omondi EO, Lin CY, Huang SM, Liao CA, Lin YP, Oliva R, van Zonneveld M. Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants. Ecol Evol 2024; 14:e11662. [PMID: 38983700 PMCID: PMC11232056 DOI: 10.1002/ece3.11662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.
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Affiliation(s)
- Emmanuel O Omondi
- Genetic Resources and Seed Unit World Vegetable Center Tainan Taiwan
| | - Chen-Yu Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | | | - Cheng-An Liao
- Department of Horticulture National Taiwan University Taipei Taiwan
| | - Ya-Ping Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | - Ricardo Oliva
- Plant Pathology World Vegetable Center Tainan Taiwan
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Camus L, Gautier M, Boitard S. Predicting species invasiveness with genomic data: Is genomic offset related to establishment probability? Evol Appl 2024; 17:e13709. [PMID: 38884022 PMCID: PMC11178484 DOI: 10.1111/eva.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/04/2024] [Indexed: 06/18/2024] Open
Abstract
Predicting the risk of establishment and spread of populations outside their native range represents a major challenge in evolutionary biology. Various methods have recently been developed to estimate population (mal)adaptation to a new environment with genomic data via so-called Genomic Offset (GO) statistics. These approaches are particularly promising for studying invasive species but have still rarely been used in this context. Here, we evaluated the relationship between GO and the establishment probability of a population in a new environment using both in silico and empirical data. First, we designed invasion simulations to evaluate the ability to predict establishment probability of two GO computation methods (Geometric GO and Gradient Forest) under several conditions. Additionally, we aimed to evaluate the interpretability of absolute Geometric GO values, which theoretically represent the adaptive genetic distance between populations from distinct environments. Second, utilizing public empirical data from the crop pest species Bactrocera tryoni, a fruit fly native from Northern Australia, we computed GO between "source" populations and a diverse range of locations within invaded areas. This practical application of GO within the context of a biological invasion underscores its potential in providing insights and guiding recommendations for future invasion risk assessment. Overall, our results suggest that GO statistics represent good predictors of the establishment probability and may thus inform invasion risk, although the influence of several factors on prediction performance (e.g., propagule pressure or admixture) will need further investigation.
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Affiliation(s)
- Louise Camus
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
| | - Simon Boitard
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
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Sun PW, Chang JT, Luo MX, Liao PC. Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change. BMC PLANT BIOLOGY 2024; 24:279. [PMID: 38609850 PMCID: PMC11015620 DOI: 10.1186/s12870-024-04942-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Climate change is expected to alter the factors that drive changes in adaptive variation. This is especially true for species with long life spans and limited dispersal capabilities. Rapid climate changes may disrupt the migration of beneficial genetic variations, making it challenging for them to keep up with changing environments. Understanding adaptive genetic variations in tree species is crucial for conservation and effective forest management. Our study used landscape genomic analyses and phenotypic traits from a thorough sampling across the entire range of Quercus longinux, an oak species native to Taiwan, to investigate the signals of adaptation within this species. RESULTS Using ecological data, phenotypic traits, and 1,933 single-nucleotide polymorphisms (SNPs) from 205 individuals, we classified three genetic groups, which were also phenotypically and ecologically divergent. Thirty-five genes related to drought and freeze resistance displayed signatures of natural selection. The adaptive variation was driven by diverse environmental pressures such as low spring precipitation, low annual temperature, and soil grid sizes. Using linear-regression-based methods, we identified isolation by environment (IBE) as the optimal model for adaptive SNPs. Redundancy analysis (RDA) further revealed a substantial joint influence of demography, geology, and environments, suggesting a covariation between environmental gradients and colonization history. Lastly, we utilized adaptive signals to estimate the genetic offset for each individual under diverse climate change scenarios. The required genetic changes and migration distance are larger in severe climates. Our prediction also reveals potential threats to edge populations in northern and southeastern Taiwan due to escalating temperatures and precipitation reallocation. CONCLUSIONS We demonstrate the intricate influence of ecological heterogeneity on genetic and phenotypic adaptation of an oak species. The adaptation is also driven by some rarely studied environmental factors, including wind speed and soil features. Furthermore, the genetic offset analysis predicted that the edge populations of Q. longinux in lower elevations might face higher risks of local extinctions under climate change.
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Affiliation(s)
- Pei-Wei Sun
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan.
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Lind BM, Candido-Ribeiro R, Singh P, Lu M, Obreht Vidakovic D, Booker TR, Whitlock MC, Yeaman S, Isabel N, Aitken SN. How useful are genomic data for predicting maladaptation to future climate? GLOBAL CHANGE BIOLOGY 2024; 30:e17227. [PMID: 38558300 DOI: 10.1111/gcb.17227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 04/04/2024]
Abstract
Methods using genomic information to forecast potential population maladaptation to climate change or new environments are becoming increasingly common, yet the lack of model validation poses serious hurdles toward their incorporation into management and policy. Here, we compare the validation of maladaptation estimates derived from two methods-Gradient Forests (GFoffset) and the risk of non-adaptedness (RONA)-using exome capture pool-seq data from 35 to 39 populations across three conifer taxa: two Douglas-fir varieties and jack pine. We evaluate sensitivity of these algorithms to the source of input loci (markers selected from genotype-environment associations [GEA] or those selected at random). We validate these methods against 2- and 52-year growth and mortality measured in independent transplant experiments. Overall, we find that both methods often better predict transplant performance than climatic or geographic distances. We also find that GFoffset and RONA models are surprisingly not improved using GEA candidates. Even with promising validation results, variation in model projections to future climates makes it difficult to identify the most maladapted populations using either method. Our work advances understanding of the sensitivity and applicability of these approaches, and we discuss recommendations for their future use.
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Affiliation(s)
- Brandon M Lind
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rafael Candido-Ribeiro
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Dragana Obreht Vidakovic
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Quebec, Canada
| | - Sally N Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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Zhou Y, Song R, Nevo E, Fu X, Wang X, Wang Y, Wang C, Chen J, Sun G, Sun D, Ren X. Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169679. [PMID: 38163608 DOI: 10.1016/j.scitotenv.2023.169679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.
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Affiliation(s)
- Yu Zhou
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruilian Song
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eviator Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
| | - Xiaoqin Fu
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengyang Wang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junpeng Chen
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Dongfa Sun
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xifeng Ren
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Andersson L, Bekkevold D, Berg F, Farrell ED, Felkel S, Ferreira MS, Fuentes-Pardo AP, Goodall J, Pettersson M. How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map. Annu Rev Anim Biosci 2024; 12:1-20. [PMID: 37906837 DOI: 10.1146/annurev-animal-021122-102933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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Affiliation(s)
- Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Edward D Farrell
- Killybegs Fishermen's Organisation, Killybegs, County Donegal, Ireland
| | - Sabine Felkel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mafalda S Ferreira
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Angela P Fuentes-Pardo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Jake Goodall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
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10
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Meger J, Ulaszewski B, Chmura DJ, Burczyk J. Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur. BMC Genomics 2024; 25:78. [PMID: 38243199 PMCID: PMC10797717 DOI: 10.1186/s12864-023-09897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change. RESULTS Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 FST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change. CONCLUSIONS The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Daniel J Chmura
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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11
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Liu Y, Wang H, Yang J, Dao Z, Sun W. Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small 'sky Island' orchid species in China. BMC PLANT BIOLOGY 2024; 24:11. [PMID: 38163918 PMCID: PMC10759615 DOI: 10.1186/s12870-023-04693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Corybas taliensis is an endemic species of sky islands in China. Its habitat is fragile and unstable, and it is likely that the species is threatened. However, it is difficult to determine the conservation priority or unit without knowing the genetic background and the overall distribution of this species. In this study, we used double digest restriction-site associated DNA-sequencing (ddRAD-seq) to investigate the conservation genomics of C. taliensis. At the same time, we modeled the extent of suitable habitat for C. taliensis in present and future (2030 and 2090) habitat using the maximum-entropy (MaxEnt) model. RESULTS The results suggested that the related C. fanjingshanensis belongs to C. taliensis and should not be considered a separate species. All the sampling locations were divided into three genetic groups: the Sichuan & Guizhou population (SG population), the Hengduan Mountains population (HD population) and Himalayan population (HM population), and we found that there was complex gene flow between the sampling locations of HD population. MT was distinct genetically from the other sampling locations due to the unique environment in Motuo. The genetic diversity (π, He) of C. taliensis was relatively high, but its contemporary effective population size (Ne) was small. C. taliensis might be currently affected by inbreeding depression, although its large population density may be able to reduce the effect of this. The predicted areas of suitable habitat currently found in higher mountains will not change significantly in the future, and these suitable habitats are predicted to spread to other higher mountains under future climate change. However, suitable habitat in relatively low altitude areas may disappear in the future. This suggests that C. taliensis will be caught in a 'summit trap' in low altitude areas, however, in contrast, the high altitude of the Himalaya and the Hengduan Mountains are predicted to act as 'biological refuges' for C. taliensis in the future. CONCLUSIONS These results not only provide a new understanding of the genetic background and potential resource distribution of C. taliensis, but also lay the foundation for its conservation and management.
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Affiliation(s)
- Yuhang Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huichun Wang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China.
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12
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Xiang X, Zhou X, Zi H, Wei H, Cao D, Zhang Y, Zhang L, Hu J. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. HORTICULTURE RESEARCH 2024; 11:uhad255. [PMID: 38274646 PMCID: PMC10809908 DOI: 10.1093/hr/uhad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.
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Affiliation(s)
- Xiaodong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xinglu Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Hantian Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Demei Cao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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13
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Hoste A, Capblancq T, Broquet T, Denoyelle L, Perrier C, Buzan E, Šprem N, Corlatti L, Crestanello B, Hauffe HC, Pellissier L, Yannic G. Projection of current and future distribution of adaptive genetic units in an alpine ungulate. Heredity (Edinb) 2024; 132:54-66. [PMID: 38082151 PMCID: PMC10798982 DOI: 10.1038/s41437-023-00661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/21/2024] Open
Abstract
Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.
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Affiliation(s)
- Amélie Hoste
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Thibaut Capblancq
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Thomas Broquet
- CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Charles Perrier
- UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000, Zagreb, Croatia
| | - Luca Corlatti
- Stelvio National Park - ERSAF Lombardia, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Barbara Crestanello
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Loïc Pellissier
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zrich, Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Glenn Yannic
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
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Lovell RSL, Collins S, Martin SH, Pigot AL, Phillimore AB. Space-for-time substitutions in climate change ecology and evolution. Biol Rev Camb Philos Soc 2023; 98:2243-2270. [PMID: 37558208 DOI: 10.1111/brv.13004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023]
Abstract
In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long-term biological data to use the past to anticipate the future, spatial climate-biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space-for-time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate-focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable - population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate-biotic relationships and (ii) the transferability of these relationships, i.e. whether climate-biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields.
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Affiliation(s)
- Rebecca S L Lovell
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Sinead Collins
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Simon H Martin
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Alex L Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Albert B Phillimore
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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Marková S, Lanier HC, Escalante MA, da Cruz MOR, Horníková M, Konczal M, Weider LJ, Searle JB, Kotlík P. Local adaptation and future climate vulnerability in a wild rodent. Nat Commun 2023; 14:7840. [PMID: 38030627 PMCID: PMC10686993 DOI: 10.1038/s41467-023-43383-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
As climate change continues, species pushed outside their physiological tolerance limits must adapt or face extinction. When change is rapid, adaptation will largely harness ancestral variation, making the availability and characteristics of that variation of critical importance. Here, we used whole-genome sequencing and genetic-environment association analyses to identify adaptive variation and its significance in the context of future climates in a small Palearctic mammal, the bank vole (Clethrionomys glareolus). We found that peripheral populations of bank vole in Britain are already at the extreme bounds of potential genetic adaptation and may require an influx of adaptive variation in order to respond. Analyses of adaptive loci suggest regional differences in climate variables select for variants that influence patterns of population adaptive resilience, including genes associated with antioxidant defense, and support a pattern of thermal/hypoxic cross-adaptation. Our findings indicate that understanding potential shifts in genomic composition in response to climate change may be key to predicting species' fate under future climates.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Hayley C Lanier
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Marcos O R da Cruz
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Mateusz Konczal
- Faculty of Biology, Evolutionary Biology Group, Adam Mickiewicz University, Poznań, Poland
| | - Lawrence J Weider
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic.
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16
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Wang TR, Meng HH, Wang N, Zheng SS, Jiang Y, Lin DQ, Song YG, Kozlowski G. Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera. ANNALS OF BOTANY 2023; 132:241-254. [PMID: 37409981 PMCID: PMC10583204 DOI: 10.1093/aob/mcad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND AND AIMS Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios. METHODS We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios. KEY RESULTS We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations. CONCLUSIONS Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.
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Affiliation(s)
- Tian-Rui Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - 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, 271018, China
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yun Jiang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Duo-Qing Lin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi-Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, Fribourg, CH-1700, Switzerland
- Natural History Museum Fribourg, Fribourg, CH-1700, Switzerland
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17
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Méndez-Cea B, García-García I, Linares JC, Gallego FJ. Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios. FRONTIERS IN PLANT SCIENCE 2023; 14:1155441. [PMID: 37636100 PMCID: PMC10451094 DOI: 10.3389/fpls.2023.1155441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023]
Abstract
Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.
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Affiliation(s)
- Belén Méndez-Cea
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel García-García
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Dpto. Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Francisco Javier Gallego
- Dpto. Genética, Fisiología y Microbiología, Unidad Docente de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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Tóth EG, Cseke K, Benke A, Lados BB, Tomov VT, Zhelev P, Kámpel JD, Borovics A, Köbölkuti ZA. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (Edinb) 2023:10.1038/s41437-023-00629-2. [PMID: 37316726 PMCID: PMC10382515 DOI: 10.1038/s41437-023-00629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
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Affiliation(s)
- Endre Gy Tóth
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Botond B Lados
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Vladimir T Tomov
- Department of Landscape Architecture, Faculty of Ecology and Landscape Architecture, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, Faculty of Forestry, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - József D Kámpel
- Ottó Herman Environmental and Agricultural Technical School, Vocational School and College (Agricultural Vocational Centre of the Kisalföld Region), Ernuszt Kelemen 1, Szombathely, 9700, Hungary
| | - Attila Borovics
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Zoltán A Köbölkuti
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
- Departement of Applied Forest Genetics Research, Bavarian Office for Forest Genetics (AWG), Forstamtsplatz 1, Teisendorf, 83317, Germany
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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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20
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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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21
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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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22
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Lin N, Liu Q, Landis JB, Rana HK, Li Z, Wang H, Sun H, Deng T. Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the
Himalaya‐Hengduan
Mountains across elevational gradients. DIVERS DISTRIB 2023. [DOI: 10.1111/ddi.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Nan Lin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- College of Life Science Henan Agricultural University Zhengzhou China
| | - Qun Liu
- School of Life Sciences Yunnan Normal University Kunming China
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium Cornell University Ithaca New York USA
- BTI Computational Biology Center Boyce Thompson Institute Ithaca New York USA
| | - Hum Kala Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Zhimin Li
- School of Life Sciences Yunnan Normal University Kunming China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
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23
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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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24
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Wortel MT, Agashe D, Bailey SF, Bank C, Bisschop K, Blankers T, Cairns J, Colizzi ES, Cusseddu D, Desai MM, van Dijk B, Egas M, Ellers J, Groot AT, Heckel DG, Johnson ML, Kraaijeveld K, Krug J, Laan L, Lässig M, Lind PA, Meijer J, Noble LM, Okasha S, Rainey PB, Rozen DE, Shitut S, Tans SJ, Tenaillon O, Teotónio H, de Visser JAGM, Visser ME, Vroomans RMA, Werner GDA, Wertheim B, Pennings PS. Towards evolutionary predictions: Current promises and challenges. Evol Appl 2023; 16:3-21. [PMID: 36699126 PMCID: PMC9850016 DOI: 10.1111/eva.13513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.
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Affiliation(s)
- Meike T. Wortel
- Swammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - Deepa Agashe
- National Centre for Biological SciencesBangaloreIndia
| | | | - Claudia Bank
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Gulbenkian Science InstituteOeirasPortugal
| | - Karen Bisschop
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Origins CenterGroningenThe Netherlands
- Laboratory of Aquatic Biology, KU Leuven KulakKortrijkBelgium
| | - Thomas Blankers
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Origins CenterGroningenThe Netherlands
| | | | - Enrico Sandro Colizzi
- Origins CenterGroningenThe Netherlands
- Mathematical InstituteLeiden UniversityLeidenThe Netherlands
| | | | | | - Bram van Dijk
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jacintha Ellers
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Astrid T. Groot
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | | | | | - Ken Kraaijeveld
- Leiden Centre for Applied BioscienceUniversity of Applied Sciences LeidenLeidenThe Netherlands
| | - Joachim Krug
- Institute for Biological PhysicsUniversity of CologneCologneGermany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of NanoscienceTU DelftDelftThe Netherlands
| | - Michael Lässig
- Institute for Biological PhysicsUniversity of CologneCologneGermany
| | - Peter A. Lind
- Department Molecular BiologyUmeå UniversityUmeåSweden
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Luke M. Noble
- Institute de Biologie, École Normale Supérieure, CNRS, InsermParisFrance
| | | | - Paul B. Rainey
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRSParisFrance
| | - Daniel E. Rozen
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Shraddha Shitut
- Origins CenterGroningenThe Netherlands
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | | | | | | | | | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Renske M. A. Vroomans
- Origins CenterGroningenThe Netherlands
- Informatics InstituteUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
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25
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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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26
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Van Daele F, Honnay O, De Kort H. Genomic analyses point to a low evolutionary potential of prospective source populations for assisted migration in a forest herb. Evol Appl 2022; 15:1859-1874. [DOI: 10.1111/eva.13485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/13/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Frederik Van Daele
- Department of Biology, Plant Conservation and Population Biology KU Leuven Leuven Belgium
| | - Olivier Honnay
- Department of Biology, Plant Conservation and Population Biology KU Leuven Leuven Belgium
| | - Hanne De Kort
- Department of Biology, Plant Conservation and Population Biology KU Leuven Leuven Belgium
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27
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DeSaix MG, George TL, Seglund AE, Spellman GM, Zavaleta ES, Ruegg KC. Forecasting climate change response in an alpine specialist songbird reveals the importance of considering novel climate. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Matthew G. DeSaix
- Department of Biology Colorado State University Fort Collins Colorado USA
| | - T. Luke George
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado USA
| | | | - Garth M. Spellman
- Department of Zoology Denver Museum of Nature and Science Denver Colorado USA
| | - Erika S. Zavaleta
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins Colorado USA
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28
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Bajpai PK, Harel A, Shafir S, Barazani O. Whole genome sequencing reveals footprints of adaptive genetic variation in populations of Eruca sativa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.938981] [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
Populations of Eruca sativa (Brassicaceae) derived from arid and Mediterranean habitats exhibit ecotypic differentiation. Here, pooled DNA sequencing was used to assess adaptive genome differentiation in the two ecotypes. Differentiated SNP loci were scanned with the empirical FST outlier method and by correlating allele frequencies with environmental parameters. Genetic diversity values were relatively higher in the pooled arid genome, whereas the pooled Mediterranean genome exhibited stronger directional selection, indicating the impact of climatic conditions on genetic diversity. GO enrichment analysis categorized the annotated differentiated loci according to biological processes, revealing a large set of candidate genes related to abiotic and biotic stress responses. Allelic variation was detected in regulatory elements and coding regions (synonymous and non-synonymous mutations) of genes belonging to different transcription factors and phytohormone signaling, suggesting adaptation to both abiotic and biotic conditions. Furthermore, SNP mutations were also found in genic regions belonging to the synthesis of secondary metabolites, including aliphatic glucosinolates and their hydrolyzed bioactive compounds, among others. The results of this eco-genomic study demonstrate the role of divergent abiotic and biotic selection factors in evolutionary processes leading to adaptive ecotypic differentiation.
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29
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Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). GLOBAL CHANGE BIOLOGY 2022; 28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.
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Affiliation(s)
- Rémi Tournebize
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Leyli Borner
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- INRAE, Le Rheu, France
| | - Stéphanie Manel
- CEFE, CNRS, EPHE-PSL University, IRD, Univ Montpellier, Montpellier, France
| | - Christine N Meynard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Yves Vigouroux
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
| | | | - Coralie Fournier
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- School of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Kassam
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- Danone Nutricia Research, Singapore
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
| | | | - Hugues Parrinello
- CNRS, INSERM, Univ. Montpellier, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | | | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | | | | | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Valérie Poncet
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
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30
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Carbeck K, Wang T, Reid JM, Arcese P. Adaptation to climate change through seasonal migration revealed by climatic versus demographic niche models. GLOBAL CHANGE BIOLOGY 2022; 28:4260-4275. [PMID: 35366358 DOI: 10.1111/gcb.16185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Predicting the geographic range of species and their response to climatic variation and change are entwined goals in conservation and evolutionary ecology. Species distribution models (SDMs) are foundational in this effort and used to visualize the geographic range of species as the spatial representation of its realized niche. SDMs are also used to forecast range shifts under climate change, but often in the absence of empirical evidence that climate limits population growth. We explored the influence of climate on demography, seasonal migration, and the extent of the geographic range in song sparrows (Melospiza melodia), a species thought to display marked local adaptation to regional climate. To do so, we developed SDMs to predict the demographic and climate niches of migratory and resident song sparrows across our study area in western North America from California to Alaska, using 48 years of demographic data from a focal population in British Columbia and 1.2 million continental-scale citizen science observations. Spatial agreement of our demographic and climate niche models in the region of our focal population was strong (76%), supporting the hypothesis that demographic performance and the occurrence of seasonal migration varied predictably with climatic conditions. In contrast, agreement at the northern (58%) and southern (40%) extents of our study area was lower, as expected if the factors limiting population growth vary regionally. Our results support the hypothesis that local climate drives spatial variation in the occurrence of seasonal migration in song sparrows by limiting the fitness of year-round residents, and suggest that climate warming has favored range expansions and facilitated an upward shift in elevational range song sparrows that forgo seasonal migration. Our work highlights the potential role of seasonal migration in climate adaptation and limits on the reliability of climate niche models not validated with demographic data.
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Affiliation(s)
- Katherine Carbeck
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tongli Wang
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jane M Reid
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Centre for Biodiversity Dynamics, Institutt for Biologi, NTNU, Trondheim, Norway
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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31
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Chai M, Tseng Y, Lu H, Luo M, Chang J, Liao P. Riding an escalator: upward range shift and patterns of genetic response to climate change in
Acer caudatifolium. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Min‐Wei Chai
- Department of Life Science National Taiwan Normal University Taipei Taiwan
| | - Yi‐Ting Tseng
- Department of Life Science National Taiwan Normal University Taipei Taiwan
- Metabolomics Core Laboratory, Healthy Aging Research Center Chang Gung University Taoyuan Taiwan
| | - Hsin‐Pei Lu
- Department of Life Science National Taiwan Normal University Taipei Taiwan
- Department of Life Science National Taiwan University Taipei Taiwan
| | - Min‐Xin Luo
- Department of Life Science National Taiwan Normal University Taipei Taiwan
| | - Jui‐Tse Chang
- Department of Life Science National Taiwan Normal University Taipei Taiwan
| | - Pei‐Chun Liao
- Department of Life Science National Taiwan Normal University Taipei Taiwan
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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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33
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Climate Adaptation, Drought Susceptibility, and Genomic-Informed Predictions of Future Climate Refugia for the Australian Forest Tree Eucalyptus globulus. FORESTS 2022. [DOI: 10.3390/f13040575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 individuals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.
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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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35
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de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, Lepelley M, Darracq O, Crouzillat D, Anten N, Musoli P, Vigouroux Y, de Kochko A, Manel S, François O, Poncet V. Adaptive potential of
Coffea canephora
from Uganda in response to climate change. Mol Ecol 2022; 31:1800-1819. [DOI: 10.1111/mec.16360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
| | - Catherine Kiwuka
- NARO Kampala Uganda
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | - Clément Gain
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | | - Cédric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Kévin Bethune
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Marie Couderc
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | | | | | | | | | | | - Niels Anten
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD Montpellier France
| | - Olivier François
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
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36
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Saleh D, Chen J, Leplé J, Leroy T, Truffaut L, Dencausse B, Lalanne C, Labadie K, Lesur I, Bert D, Lagane F, Morneau F, Aury J, Plomion C, Lascoux M, Kremer A. Genome-wide evolutionary response of European oaks during the Anthropocene. Evol Lett 2022; 6:4-20. [PMID: 35127134 PMCID: PMC8802238 DOI: 10.1002/evl3.269] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long-lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.
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Affiliation(s)
- Dounia Saleh
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Jun Chen
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | | | - Thibault Leroy
- Department of Botany and Biodiversity ResearchUniversity of ViennaVienna1010Austria
| | - Laura Truffaut
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | | | - Céline Lalanne
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Karine Labadie
- Genoscope, Institut de Biologie François Jacob, Commissariat à l’énergie atomique (CEA)Université de Paris‐SaclayEvry91057France
| | | | - Didier Bert
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | | | - François Morneau
- Département Recherche Développement InnovationOffice National des ForêtsBoigny‐Sur‐Bionne45760France,Current Address: Service de l'Information Statistique Forestière et EnvironnementaleInstitut National de l'Information géographique et ForestièreNogent‐sur‐Vernisson45290France
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRSUniv Evry, Université Paris‐SaclayEvry91057France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSE‐75236Sweden
| | - Antoine Kremer
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
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37
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Liang YY, Shi Y, Yuan S, Zhou BF, Chen XY, An QQ, Ingvarsson PK, Plomion C, Wang B. Linked selection shapes the landscape of genomic variation in three oak species. THE NEW PHYTOLOGIST 2022; 233:555-568. [PMID: 34637540 DOI: 10.1111/nph.17793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('FST -islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that FST -islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
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Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | | | - Baosheng Wang
- 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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38
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Feng L, Du FK. Landscape Genomics in Tree Conservation Under a Changing Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:822217. [PMID: 35283901 PMCID: PMC8908315 DOI: 10.3389/fpls.2022.822217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/10/2022] [Indexed: 05/11/2023]
Abstract
Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fang K. Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Fang K. Du,
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39
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Aavik T, Träger S, Zobel M, Honnay O, Van Geel M, Bueno CG, Koorem K. The joint effect of host plant genetic diversity and arbuscular mycorrhizal fungal communities on restoration success. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsipe Aavik
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Sabrina Träger
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
- Institute of Biology/Geobotany and Botanical Garden Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Martin Zobel
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Olivier Honnay
- Plant Conservation and Population Biology Biology Department University of Leuven Heverlee Belgium
| | - Maarten Van Geel
- Plant Conservation and Population Biology Biology Department University of Leuven Heverlee Belgium
| | - C. Guillermo Bueno
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Kadri Koorem
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
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40
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Impact of Gene Flow and Introgression on the Range Wide Genetic Structure of Quercus robur (L.) in Europe. FORESTS 2021. [DOI: 10.3390/f12101425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.
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41
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Capblancq T, Forester BR. Redundancy analysis: A Swiss Army Knife for landscape genomics. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13722] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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42
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Postolache D, Oddou-Muratorio S, Vajana E, Bagnoli F, Guichoux E, Hampe A, Le Provost G, Lesur I, Popescu F, Scotti I, Piotti A, Vendramin GG. Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range. Mol Ecol 2021; 30:5029-5047. [PMID: 34383353 DOI: 10.1111/mec.16115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.
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Affiliation(s)
- D Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Romania
| | - S Oddou-Muratorio
- INRAE, URFM, Avignon, France.,ECOBIOP Université de Pau et des Pays de l'Adour, INRAE, ECOBIOP, E2S UPPA, Saint-Pée-sur-Nivelle, France
| | - E Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Firenze), Italy
| | - E Guichoux
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France
| | - A Hampe
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France
| | - G Le Provost
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France
| | - I Lesur
- Université de Bordeaux, INRAE, BIOGECO, Cestas, France.,HelixVenture, Mérignac, France
| | - F Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Romania
| | | | - A Piotti
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Firenze), Italy
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Firenze), Italy
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43
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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Abstract
Quercus species (oaks) have been an integral part of the landscape in the northern hemisphere for millions of years. Their ability to adapt and spread across different environments and their contributions to many ecosystem services is well documented. Human activity has placed many oak species in peril by eliminating or adversely modifying habitats through exploitative land usage and by practices that have exacerbated climate change. The goal of this review is to compile a list of oak species of conservation concern, evaluate the genetic data that is available for these species, and to highlight the gaps that exist. We compiled a list of 124 Oaks of Concern based on the Red List of Oaks 2020 and the Conservation Gap Analysis for Native U.S. Oaks and their evaluations of each species. Of these, 57% have been the subject of some genetic analysis, but for most threatened species (72%), the only genetic analysis was done as part of a phylogenetic study. While nearly half (49%) of published genetic studies involved population genetic analysis, only 16 species of concern (13%) have been the subject of these studies. This is a critical gap considering that analysis of intraspecific genetic variability and genetic structure are essential for designing conservation management strategies. We review the published population genetic studies to highlight their application to conservation. Finally, we discuss future directions in Quercus conservation genetics and genomics.
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Seaborn T, Andrews KR, Applestein CV, Breech TM, Garrett MJ, Zaiats A, Caughlin TT. Integrating genomics in population models to forecast translocation success. Restor Ecol 2021. [DOI: 10.1111/rec.13395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Travis Seaborn
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID U.S.A
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID U.S.A
| | | | - Tyler M. Breech
- Department of Biological Sciences Idaho State University Pocatello ID U.S.A
| | - Molly J. Garrett
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID U.S.A
| | - Andrii Zaiats
- Biological Sciences Boise State University Boise ID U.S.A
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Rellstab C, Dauphin B, Exposito‐Alonso M. Prospects and limitations of genomic offset in conservation management. Evol Appl 2021; 14:1202-1212. [PMID: 34025760 PMCID: PMC8127717 DOI: 10.1111/eva.13205] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
In nature conservation, there is keen interest in predicting how populations will respond to environmental changes such as climate change. These predictions can help determine whether a population can be self-sustaining under future alterations of its habitat or whether it may require human intervention such as protection, restoration, or assisted migration. An increasingly popular approach in this respect is the concept of genomic offset, which combines genomic and environmental data from different time points and/or locations to assess the degree of possible maladaptation to new environmental conditions. Here, we argue that the concept of genomic offset holds great potential, but an exploration of its risks and limitations is needed to use it for recommendations in conservation or assisted migration. After briefly describing the concept, we list important issues to consider (e.g., statistical frameworks, population genetic structure, migration, independent evidence) when using genomic offset or developing these methods further. We conclude that genomic offset is an area of development that still lacks some important features and should be used in combination with other approaches to inform conservation measures.
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Affiliation(s)
| | | | - Moises Exposito‐Alonso
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCAUSA
- Department of BiologyStanford UniversityStanfordCAUSA
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Qian C, Yan X, Fang T, Yin X, Zhou S, Fan X, Chang Y, Ma XF. Genomic Adaptive Evolution of Sand Rice ( Agriophyllum squarrosum) and Its Implications for Desert Ecosystem Restoration. Front Genet 2021; 12:656061. [PMID: 33995487 PMCID: PMC8120313 DOI: 10.3389/fgene.2021.656061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/08/2021] [Indexed: 01/13/2023] Open
Abstract
Natural selection is a significant driver of population divergence and speciation of plants. Due to local adaptation to geographic regions with ecological gradients, plant populations harbored a wide range of adaptive genetic variation to enable them to survive the heterogeneous habitats. This is all the more necessary for desert plants, as they must tolerant more striking gradients of abiotic stresses. However, the genomic mechanism by which desert plants adapt to ecological heterogeneity remains unclear, which could help to guide the sustainability of desert ecosystems. Here, using restriction-site-associated DNA sequencing in 38 natural populations, we investigated the genomic divergence and environmental adaptation of sand rice, Agriophyllum squarrosum, an annual pioneer species that covers sand dunes in northern China. Population genetic structure analyses showed that sand rice could be divided into three geographically distinct lineages, namely, Northwest, Central, and East. Phylogeographic analyses revealed that the plant might originate locally in Bergen County and further differentiated into the East lineage and then the Central lineage. Ecological niche modeling found that different lineages occupied distinct ecological niches, suggesting that the ecological gradient would have triggered genomic differentiation among sand rice lineages. Ecological association study supported that the three SNPs under divergent selection were closely correlated with precipitation gradients, indicating that precipitation might be the most important stress trigger for lineage diversity in sand rice. These adaptive SNPs could be used to genotype suitable germplasms for the ecological restoration of specific desertified lands. Further analyses found that genetic structure could significantly overestimate the signals for balancing selection. Within the Central lineage, we still found that 175 SNPs could be subject to balancing selection, which could be the means by which sand rice maintains genetic diversity and adapts to multiple stresses across heterogeneous deserts and sandy lands. From a genomic point of view, this study highlighted the local and global adaptation patterns of a desert plant to extreme and heterogeneous habitats. Our data provide molecular guidance for the restoration of desertified lands in the arid and semi-arid regions of China and could facilitate the marker assistant breeding of this potential crop to mitigate climate change.
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Affiliation(s)
- Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xia Yan
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Eco-hydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Tingzhou Fang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyue Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Zhou
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xingke Fan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- School of Life Sciences, Nantong University, Nantong, China
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48
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von Takach B, Ahrens CW, Lindenmayer DB, Banks SC. Scale-dependent signatures of local adaptation in a foundation tree species. Mol Ecol 2021; 30:2248-2261. [PMID: 33740830 DOI: 10.1111/mec.15894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023]
Abstract
Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.
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Affiliation(s)
- Brenton von Takach
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia.,Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - David B Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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49
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Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis. FORESTS 2021. [DOI: 10.3390/f12030364] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.
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50
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Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021; 113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
Abstract
China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China; School of Biological Science and Technology, Baotou Teachers' College, Baotou, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
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