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Ahrens CW, Murray K, Mazanec RA, Ferguson S, Jones A, Tissue DT, Byrne M, Borevitz JO, Rymer PD. Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla. BMC Genomics 2024; 25:640. [PMID: 38937661 PMCID: PMC11209971 DOI: 10.1186/s12864-024-10531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. RESULTS We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. CONCLUSIONS Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
- Cesar Australia, Brunswick, VIC, 3058, Australia.
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Richard A Mazanec
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024; 24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [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: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Annie S Guillaume
- Geospatial Molecular Epidemiology group (GEOME), Laboratory for Biological Geochemistry (LGB), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arianna Kuhn
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- Virginia Museum of Natural History, Martinsville, Virginia, USA
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, Western Australia, Australia
| | - Ted Cosart
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Leif Howard
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Shawn R Narum
- Hagerman Genetics Lab, University of Idaho, Hagerman, Idaho, USA
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Helen R Taylor
- Royal Zoological Society of Scotland, Edinburgh, Scotland
| | - Gregg W C Thomas
- Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Maren Wellenreuther
- Plant and Food Research, Nelson, New Zealand
- University of Auckland, Auckland, New Zealand
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
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Fu PC, Twyford AD, Hao YT, Zhang Y, Chen SL, Sun SS. Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai-Tibet Plateau. ANNALS OF BOTANY 2023; 132:1271-1288. [PMID: 37963010 PMCID: PMC10902892 DOI: 10.1093/aob/mcad179] [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: 06/21/2023] [Revised: 10/19/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND AND AIMS Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP). METHODS We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy. KEY RESULTS Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance. CONCLUSIONS This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Alex D Twyford
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Yu-Tong Hao
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Yue Zhang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810001 Xining, P. R. China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
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Nimbs MJ, Champion C, Lobos SE, Malcolm HA, Miller AD, Seinor K, Smith SD, Knott N, Wheeler D, Coleman MA. Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change. PeerJ 2023; 11:e16498. [PMID: 38025735 PMCID: PMC10676721 DOI: 10.7717/peerj.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.
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Affiliation(s)
- Matt J. Nimbs
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Curtis Champion
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Simon E. Lobos
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Hamish A. Malcolm
- NSW Department of Primary Industries, Fisheries Research, Coffs Harbour, NSW, Australia
| | - Adam D. Miller
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Kate Seinor
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Stephen D.A. Smith
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Aquamarine Australia, Mullaway, NSW, Australia
| | - Nathan Knott
- NSW Department of Primary Industries, Fisheries Research, Huskisson, NSW, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange, NSW, Australia
| | - Melinda A. Coleman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
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5
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Lin YP, Lu CY, Lee CR. The Past Contribution and Future Fate of Genetic Variants under Climate Change in an Island Population of Musa itinerans. Am Nat 2023; 202:558-570. [PMID: 37792919 DOI: 10.1086/726015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractGenetic variation within species is crucial for sessile species to adapt to novel environments when facing dramatic climate changes. However, the debate continues whether standing ancestral variation adaptive to current environmental variability is sufficient to guarantee future suitability. Using wild banana Musa itinerans, we investigated the relative contribution of standing ancestral variation versus new mutations to environmental adaptation and inferred their future fate. On the continental island of Taiwan, local populations immigrated from the Southeast Asian continent during the ice age and have been isolated since then. This allows the classification of genetic variants into standing ancestral variation (polymorphic in Taiwan and the continent) and new mutations (polymorphic only in Taiwan). For temperature-related variables where Taiwan is mainly within the ancestral climatic range, standing ancestral variation had a slightly stronger association than new mutations. New mutations were more important for precipitation-related variables, where northeastern Taiwan had much more winter rainfall than most of continental Southeast Asia. Upon future climate change, new mutations showed higher genetic offset in regions of abrupt transition between allele frequency and local environments, suggesting their greater spatial heterogeneity of future vulnerability.
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Filipe JC, Ahrens CC, Byrne M, Hardy G, Rymer PD. Germination temperature sensitivity differs between co-occurring tree species and climate origins resulting in contrasting vulnerability to global warming. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:146-162. [PMID: 37362420 PMCID: PMC10290426 DOI: 10.1002/pei3.10108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/20/2023] [Accepted: 04/04/2023] [Indexed: 06/28/2023]
Abstract
Climate change is shifting temperatures from historical patterns, globally impacting forest composition and resilience. Seed germination is temperature-sensitive, making the persistence of populations and colonization of available habitats vulnerable to warming. This study assessed germination response to temperature in foundation trees in south-western Australia's Mediterranean-type climate forests (Eucalyptus marginata (jarrah) and Corymbia calophylla (marri)) to estimate the thermal niche and vulnerability among populations. Seeds from the species' entire distribution were collected from 12 co-occurring populations. Germination thermal niche was investigated using a thermal gradient plate (5-40°C). Five constant temperatures between 9 and 33°C were used to test how the germination niche (1) differs between species, (2) varies among populations, and (3) relates to the climate of origin. Germination response differed among species; jarrah had a lower optimal temperature and thermal limit than marri (T o 15.3°C, 21.2°C; ED50 23.4°C, 31°C, respectively). The thermal limit for germination differed among populations within both species, yet only marri showed evidence for adaptation to thermal origins. While marri has the capacity for germination at higher thermal temperatures, jarrah is more vulnerable to global warming exceeding safety margins. This discrepancy is predicted to alter species distributions and forest composition in the future.
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Affiliation(s)
- João C. Filipe
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
- Centre for Terrestrial Ecosystem Science and SustainabilityHarry Butler InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Collin C. Ahrens
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Research Centre for Ecosystem ResilienceRoyal Botanic Gardens and Domain TrustSydneyNew South WalesAustralia
- Cesar AustraliaBrunswickVictoriaAustralia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
| | - Giles Hardy
- Centre for Terrestrial Ecosystem Science and SustainabilityHarry Butler InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Paul D. Rymer
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
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7
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Zhao D, Zhang J, Hui N, Wang L, Tian Y, Ni W, Long J, Jiang L, Li Y, Diao S, Li J, Tembrock LR, Wu Z, Wang Z. A Genomic Quantitative Study on the Contribution of the Ancestral-State Bases Relative to Derived Bases in the Divergence and Local Adaptation of Populus davidiana. Genes (Basel) 2023; 14:genes14040821. [PMID: 37107579 PMCID: PMC10137690 DOI: 10.3390/genes14040821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan-Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai-Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region.
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Affiliation(s)
- Dandan Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Collaborative Innovation Center of Sustainable, Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Nan Hui
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Li Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yang Tian
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wanning Ni
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jinhua Long
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Li Jiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yi Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jinhua Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Collaborative Innovation Center of Sustainable, Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Li Y, Wang SC, Li Q, Li MW, Mao RL, Zhang HC, Yuan WJ, Quan J. Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia. Genetica 2023; 151:47-59. [PMID: 36436173 DOI: 10.1007/s10709-022-00176-4] [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: 06/16/2022] [Accepted: 11/23/2022] [Indexed: 11/28/2022]
Abstract
Identifying cold-related genes can provide insights into the cold adaptation mechanism of weeping forsythia. In this study, we compared the changes in gene expressions and physiological and biochemical indices under short-term cold stimulation with the changes in gene sequences under a long-term heterogeneous environment to investigate the cold adaptation mechanism in weeping forsythia. The data of adaptive gene sequence changes, e.g., single nucleotide polymorphisms, were obtained from previous landscape genomics studies. The physiological and biochemical indicators and transcriptome results showed that weeping forsythia initiated a series of programs, including increasing cell osmotic pressures, scavenging ROS, activating the defense mechanism that crosses with pathogen infection, and upregulating CBF/DREB1 transcription factor 1, to cope with short-term cold stress. A reanalysis of landscape genomic data suggested that weeping forsythia responded to long-term heterogeneous cold stress by the differentiation of genes related to synthesis of aromatic substances and adenosine triphosphate. Our results supported the hypothesis that the adaptation mechanisms of species to short-term environmental stimulation and long-term stress in heterogeneous environments are different. The differences in cold tolerance among populations are not necessarily obtained by changing cold-responsive gene sequences. This study provides new insights into the cold adaptation mechanisms of plants.
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Affiliation(s)
- Yong Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China.,State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Shu-Chen Wang
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Qian Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Ming-Wan Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Run-Li Mao
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - He-Chen Zhang
- Horticultural Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wang-Jun Yuan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Jine Quan
- College of Forestry, Henan Agricultural University, Zhengzhou, China.
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9
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Wang Y, Zhang L, Zhou Y, Ma W, Li M, Guo P, Feng L, Fu C. Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China. Front Genet 2023; 14:1150704. [PMID: 37144128 PMCID: PMC10151583 DOI: 10.3389/fgene.2023.1150704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.
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Affiliation(s)
- Yihan Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Lin Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Yuchao Zhou
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Wenxin Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Manyu Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Peng Guo
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
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10
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Ahrens CW, Watson‐Lazowski A, Huang G, Tissue DT, Rymer PD. The roles of divergent and parallel molecular evolution contributing to thermal adaptive strategies in trees. PLANT, CELL & ENVIRONMENT 2022; 45:3476-3491. [PMID: 36151708 PMCID: PMC9828096 DOI: 10.1111/pce.14449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Local adaptation is a driver of biological diversity, and species may develop analogous (parallel evolution) or alternative (divergent evolution) solutions to similar ecological challenges. We expect these adaptive solutions would culminate in both phenotypic and genotypic signals. Using two Eucalyptus species (Eucalyptus grandis and Eucalyptus tereticornis) with overlapping distributions grown under contrasting 'local' temperature conditions to investigate the independent contribution of adaptation and plasticity at molecular, physiological and morphological levels. The link between gene expression and traits markedly differed between species. Divergent evolution was the dominant pattern driving adaptation (91% of all significant genes); but overlapping gene (homologous) responses were dependent on the determining factor (plastic, adaptive or genotype by environment interaction). Ninety-eight percent of the plastic homologs were similarly regulated, while 50% of the adaptive homologs and 100% of the interaction homologs were antagonistical. Parallel evolution for the adaptive effect in homologous genes was greater than expected but not in favour of divergent evolution. Heat shock proteins for E. grandis were almost entirely driven by adaptation, and plasticity in E. tereticornis. These results suggest divergent molecular evolutionary solutions dominated the adaptive mechanisms among species, even in similar ecological circumstances. Suggesting that tree species with overlapping distributions are unlikely to equally persist in the future.
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Affiliation(s)
- Collin W. Ahrens
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Research Centre for Ecosystem ResilienceRoyal Botanic Gardens and Domain TrustSydneyNew South WalesAustralia
| | - Alexander Watson‐Lazowski
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- John Innes CentreNorwich Research ParkNorwichUK
| | - Guomin Huang
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
| | - David T. Tissue
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- Global Centre for Land‐Based Innovation, Hawkesbury CampusWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Paul D. Rymer
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
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11
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Fu P, Favre A, Wang R, Huang Y, Sun S. Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau. BMC PLANT BIOLOGY 2022; 22:504. [PMID: 36307765 PMCID: PMC9615307 DOI: 10.1186/s12870-022-03879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth. Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region. RESULTS Combining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species. CONCLUSION Our study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.
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Affiliation(s)
- Pengcheng Fu
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Adrien Favre
- Regional nature park of the Trient Valley, La Place 24, 1922, Salvan, Switzerland
| | - Rui Wang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Yizhuo Huang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Shanshan Sun
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China.
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12
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Challis A, Blackman C, Ahrens C, Medlyn B, Rymer P, Tissue D. Adaptive plasticity in plant traits increases time to hydraulic failure under drought in a foundation tree. TREE PHYSIOLOGY 2022; 42:708-721. [PMID: 34312674 DOI: 10.1093/treephys/tpab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
The viability of forest trees, in response to climate change-associated drought, will depend on their capacity to survive through genetic adaptation and phenotypic plasticity in drought tolerance traits. Genotypes with enhanced plasticity for drought tolerance (adaptive plasticity) will have a greater ability to persist and delay the onset of hydraulic failure. By examining populations from different climate-origins grown under contrasting soil water availability, we tested for genotype (G), environment (E) and genotype-by-environment (G × E) effects on traits that determine the time it takes for saplings to desiccate from stomatal closure to 88% loss of stem hydraulic conductance (time to hydraulic failure, THF). Specifically, we hypothesized that: (i) THF is dependent on a G × E interaction, with longer THF for warm, dry climate populations in response to chronic water deficit treatment compared with cool, wet populations, and (ii) hydraulic and allometric traits explain the observed patterns in THF. Corymbia calophylla saplings from two populations originating from contrasting climates (warm-dry or cool-wet) were grown under well-watered and chronic soil water deficit treatments in large containers. Hydraulic and allometric traits were measured and then saplings were dried-down to critical levels of drought stress to estimate THF. Significant plasticity was detected in the warm-dry population in response to water-deficit, with enhanced drought tolerance compared with the cool-wet population. Projected leaf area and total plant water storage showed treatment variation, and minimum conductance showed significant population differences driving longer THF in trees from warm-dry origins grown in water-limited conditions. Our findings contribute information on intraspecific variation in key drought traits, including hydraulic and allometric determinants of THF. It highlights the need to quantify adaptive capacity in populations of forest trees in climate change-type drought to improve predictions of forest die-back.
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Affiliation(s)
- Anthea Challis
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Chris Blackman
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Collin Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Belinda Medlyn
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Paul Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - David Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
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13
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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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14
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Liang S, Zhang X, Wei R. Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Mol Ecol 2022; 31:2679-2697. [DOI: 10.1111/mec.16420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Si‐Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
- University of Chinese Academy of Sciences College of Life Sciences Beijing 100049 China
| | - Xian‐Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
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15
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Filipe JC, Rymer PD, Byrne M, Hardy G, Mazanec R, Ahrens CW. Signatures of natural selection in a foundation tree along Mediterranean climatic gradients. Mol Ecol 2022; 31:1735-1752. [PMID: 35038378 PMCID: PMC9305101 DOI: 10.1111/mec.16351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 11/30/2022]
Abstract
Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean‐type climates (MTC). Forest management that enhance forests’ resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex. For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South‐west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype‐association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (FST = 0.04), environmental association analyses found a total of 2336 unique SNPs associated with temperature and precipitation variables, with 1440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.
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Affiliation(s)
- J C Filipe
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University
| | - P D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University
| | - M Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions
| | - G Hardy
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University
| | - R Mazanec
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions
| | - C W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University
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16
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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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17
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Ahrens CW, Challis A, Byrne M, Leigh A, Nicotra AB, Tissue D, Rymer P. Repeated extreme heatwaves result in higher leaf thermal tolerances and greater safety margins. THE NEW PHYTOLOGIST 2021; 232:1212-1225. [PMID: 34292598 DOI: 10.1111/nph.17640] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
The frequency and severity of heatwave events are increasing, exposing species to conditions beyond their physiological limits. Species respond to heatwaves in different ways, however it remains unclear if plants have the adaptive capacity to successfully respond to hotter and more frequent heatwaves. We exposed eight tree populations from two climate regions grown under cool and warm temperatures to repeated heatwave events of moderate (40°C) and extreme (46°C) severity to assess adaptive capacity to heatwaves. Leaf damage and maximum quantum efficiency of photosystem II (Fv /Fm ) were significantly impacted by heatwave severity and growth temperatures, respectively; populations from a warm-origin avoided damage under moderate heatwaves compared to those from a cool-origin, indicating a degree of local adaptation. We found that plasticity to heatwave severity and repeated heatwaves contributed to enhanced thermal tolerance and lower leaf temperatures, leading to greater thermal safety margins (thermal tolerance minus leaf temperature) in a second heatwave. Notably, while we show that adaptation and physiological plasticity are important factors affecting plant adaptive capacity to thermal stress, plasticity of thermal tolerances and thermal safety margins provides the opportunity for trees to persist among fluctuating heatwave exposures.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Anthea Challis
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Bentley Delivery Centre, Locked Bag 104, Bentley, WA, 6983, Australia
| | - Andrea Leigh
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Adrienne B Nicotra
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - David Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Paul Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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18
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Li J, Zeng Y, Pan Y, Zhou L, Zhang Z, Guo H, Lou Q, Shui G, Huang H, Tian H, Guo Y, Yuan P, Yang H, Pan G, Wang R, Zhang H, Yang S, Guo Y, Ge S, Li J, Li Z. Stepwise selection of natural variations at CTB2 and CTB4a improves cold adaptation during domestication of japonica rice. THE NEW PHYTOLOGIST 2021; 231:1056-1072. [PMID: 33892513 DOI: 10.1111/nph.17407] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP-glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica. CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high-altitude to high-latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.
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Affiliation(s)
- Jilong Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yawen Zeng
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yinghua Pan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Lei Zhou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qijin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Lipid ALL Technologies Ltd, Changzhou, 213000, China
| | - Hanguang Huang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - He Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongmei Guo
- Institute of Crop Science, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Pingrong Yuan
- Institute of Crop Science, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Hong Yang
- Lijiang Institute of Agricultural Science, Lijiang, 674100, China
| | - Guojun Pan
- Rice Research Institute, Heilongjiang Academy of Agricultural Science, Jiamusi, 154026, China
| | - Ruiying Wang
- Rice Research Institute, Heilongjiang Academy of Agricultural Science, Jiamusi, 154026, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Li Y, Shi LC, Pei NC, Cushman SA, Si YT. Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. BMC PLANT BIOLOGY 2021; 21:273. [PMID: 34130656 PMCID: PMC8204298 DOI: 10.1186/s12870-021-03075-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/26/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. RESULTS Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation-reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. CONCLUSIONS Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.
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Affiliation(s)
- Yong Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Long-Chen Shi
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Nan-Cai Pei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, AZ USA
| | - Yu-Tao Si
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
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20
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Seaborn T, Griffith D, Kliskey A, Caudill CC. Building a bridge between adaptive capacity and adaptive potential to understand responses to environmental change. GLOBAL CHANGE BIOLOGY 2021; 27:2656-2668. [PMID: 33666302 DOI: 10.1111/gcb.15579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Adaptive capacity is a topic at the forefront of environmental change research with roots in both social, ecological, and evolutionary science. It is closely related to the evolutionary biology concept of adaptive potential. In this systematic literature review, we: (1) summarize the history of these topics and related fields; (2) assess relationship(s) between the concepts among disciplines and the use of the terms in climate change research, and evaluate methodologies, metrics, taxa biases, and the geographic scale of studies; and (3) provide a synthetic conceptual framework to clarify concepts. Bibliometric analyses revealed the terms have been used most frequently in conservation and evolutionary biology journals, respectively. There has been a greater growth in studies of adaptive potential than adaptive capacity since 2001, but a greater geographical extent of adaptive capacity studies. Few studies include both, and use is often superficial. Our synthesis considers adaptive potential as one process contributing to adaptive capacity of complex systems, notes "sociological" adaptive capacity definitions include actions aimed at desired outcome (i.e., policies) as a system driver whereas "biological" definitions exclude such drivers, and suggests models of adaptive capacity require integration of evolutionary and social-ecological system components.
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Affiliation(s)
- Travis Seaborn
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - David Griffith
- Center for Resilient Communities, University of Idaho, Moscow, ID, USA
| | - Andrew Kliskey
- Center for Resilient Communities, University of Idaho, Moscow, ID, USA
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Binks RM, Steane DA, Byrne M. Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris. Ecol Evol 2021; 11:5096-5110. [PMID: 34025994 PMCID: PMC8131811 DOI: 10.1002/ece3.7403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non-contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.
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Affiliation(s)
- Rachel M. Binks
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
| | - Dorothy A. Steane
- School of Natural Sciences and ARC Training Centre for Forest ValueUniversity of TasmaniaHobartTasmaniaAustralia
- CSIRO Land and WaterSandy BayTasmaniaAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
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22
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Bennett KL, McMillan WO, Loaiza JR. The genomic signal of local environmental adaptation in Aedes aegypti mosquitoes. Evol Appl 2021; 14:1301-1313. [PMID: 34025769 PMCID: PMC8127705 DOI: 10.1111/eva.13199] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
Local adaptation is important when predicting arthropod-borne disease risk because of its impacts on vector population fitness and persistence. However, the extent that vector populations are adapted to the environment generally remains unknown. Despite low population structure and high gene flow in Aedes aegypti mosquitoes across Panama, excepting the province of Bocas del Toro, we identified 128 candidate SNPs, clustered within 17 genes, which show a strong genomic signal of local environmental adaptation. This putatively adaptive variation occurred across fine geographical scales with the composition and frequency of candidate adaptive loci differing between populations in wet tropical environments along the Caribbean coast and dry tropical conditions typical of the Pacific coast. Temperature and vegetation were important predictors of adaptive genomic variation in Ae. aegypti with several potential areas of local adaptation identified. Our study lays the foundations of future work to understand whether environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and whether this could either aid or hinder efforts of population control.
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Affiliation(s)
- Kelly L. Bennett
- Smithsonian Tropical Research InstituteBalboa AnconRepublic of Panama
| | - W. Owen McMillan
- Smithsonian Tropical Research InstituteBalboa AnconRepublic of Panama
| | - Jose R. Loaiza
- Smithsonian Tropical Research InstituteBalboa AnconRepublic of Panama
- Instituto de Investigaciones Científicas y Servicios de Alta TecnologíaPanamáRepublic of Panama
- Programa Centroamericano de Maestría en EntomologíaUniversidad de PanamáPanamáRepublic of Panama
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23
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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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24
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Degen B, Yanbaev YA, Ianbaev RY, Bakhtina SY, Gabitova AA, Tagirova AA. Genetic Diversity and Differentiation of Northern Populations of Pedunculate Oak Based on Analysis of New SNP Markers. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421030054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Ahrens CW, Jordan R, Bragg J, Harrison PA, Hopley T, Bothwell H, Murray K, Steane DA, Whale JW, Byrne M, Andrew R, Rymer PD. Regarding the F-word: The effects of data filtering on inferred genotype-environment associations. Mol Ecol Resour 2021; 21:1460-1474. [PMID: 33565725 DOI: 10.1111/1755-0998.13351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023]
Abstract
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results, negatively affecting management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for assessment of adaptation to environment. We use empirical and simulated data sets derived from two widespread tree species to assess the effects of filtering on GEA outputs. Critically, we find that the level of filtering of missing data and minor allele frequency affect the identification of true positives. Even slight adjustments to these thresholds can change the rate of true positive detection. Using conservative thresholds for missing data and minor allele frequency substantially reduces the size of the data set, lessening the power to detect adaptive variants (i.e., simulated true positives) with strong and weak strengths of selection. Regardless, strength of selection was a good predictor for GEA detection, but even some SNPs under strong selection went undetected. False positive rates varied depending on the species and GEA method, and filtering significantly impacted the predictions of adaptive capacity in downstream analyses. We make several recommendations regarding filtering for GEA methods. Ultimately, there is no filtering panacea, but some choices are better than others, depending on the study system, availability of genomic resources, and desired objectives.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | - Jason Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, NSW, Australia
| | - Peter A Harrison
- School of Natural Sciences and Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tas., Australia
| | - Tara Hopley
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, WA, Australia
| | | | - Kevin Murray
- Australian National University, Acton, ACT, Australia
| | - Dorothy A Steane
- CSIRO Land & Water, Hobart, Tas., Australia.,School of Natural Sciences and Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tas., Australia
| | - John W Whale
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, WA, Australia
| | - Rose Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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26
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Zhang X, Sun Y, Landis JB, Zhang J, Yang L, Lin N, Zhang H, Guo R, Li L, Zhang Y, Deng T, Sun H, Wang H. Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales). THE NEW PHYTOLOGIST 2020; 228:285-301. [PMID: 32426908 DOI: 10.1111/nph.16669] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/08/2020] [Indexed: 05/25/2023]
Abstract
Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance. Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92507, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
| | - Jianwen Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Linsen Yang
- Hubei Key Laboratory of Shennongjia Golden Monkey Conservation Biology, Administration of Shennongjia National Park, Shennongjia, Hubei, 442400, China
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yonghong Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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27
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Ahrens CW, James EA, Miller AD, Scott F, Aitken NC, Jones AW, Lu-Irving P, Borevitz JO, Cantrill DJ, Rymer PD. Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra. Mol Ecol 2020; 29:3872-3888. [PMID: 32885504 DOI: 10.1111/mec.15614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022]
Abstract
Global climate change poses a significant threat to natural communities around the world, with many plant species showing signs of climate stress. Grassland ecosystems are not an exception, with climate change compounding contemporary pressures such as habitat loss and fragmentation. In this study, we assess the climate resilience of Themeda triandra, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates. We explicitly quantified isolation by distance (IBD) and isolation by environment (IBE) and predicted genomic vulnerability of populations to future climates based on expected deviation from current genomic composition. We found that a majority (54%) of genomic variation could be attributed to IBD, while an additional 22% (27% when including ploidy information) could be explained by two temperature and two precipitation climate variables demonstrating IBE. Ploidy polymorphisms were common within populations (31/52 populations), indicating that ploidy mixing is characteristic of T. triandra populations. Genomic vulnerabilities were found to be heterogeneously distributed throughout the landscape, and our analysis suggested that ploidy polymorphism, along with other factors linked to polyploidy, reduced vulnerability to future climates by 60% (0.25-0.10). Our data suggests that polyploidy may facilitate adaptation to hotter climates and highlight the importance of incorporating ploidy in adaptive management strategies to promote the resilience of this and other foundation species.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia.,Royal Botanic Gardens Victoria, Melbourne, VIC, Australia
| | | | - Adam D Miller
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Warrnambool, VIC, Australia
| | - Ferguson Scott
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ashley W Jones
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Garden, Sydney, NSW, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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28
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Mostert-O'Neill MM, Reynolds SM, Acosta JJ, Lee DJ, Borevitz JO, Myburg AA. Genomic evidence of introgression and adaptation in a model subtropical tree species, Eucalyptus grandis. Mol Ecol 2020; 30:625-638. [PMID: 32881106 DOI: 10.1111/mec.15615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 11/27/2022]
Abstract
The genetic consequences of adaptation to changing environments can be deciphered using population genomics, which may help predict species' responses to global climate change. Towards this, we used genome-wide SNP marker analysis to determine population structure and patterns of genetic differentiation in terms of neutral and adaptive genetic variation in the natural range of Eucalyptus grandis, a widely cultivated subtropical and temperate species, serving as genomic reference for the genus. We analysed introgression patterns at subchromosomal resolution using a modified ancestry mapping approach and identified provenances with extensive interspecific introgression in response to increased aridity. Furthermore, we describe potentially adaptive genetic variation as explained by environment-associated SNP markers, which also led to the discovery of what is likely a large structural variant. Finally, we show that genes linked to these markers are enriched for biotic and abiotic stress responses.
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Affiliation(s)
- Marja Mirjam Mostert-O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sharon Melissa Reynolds
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Juan Jose Acosta
- Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - David John Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, Australia
| | - Justin O Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT, Australia
| | - Alexander Andrew Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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29
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Li LF, Cushman SA, He YX, Li Y. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia. HORTICULTURE RESEARCH 2020; 7:130. [PMID: 32821413 PMCID: PMC7395120 DOI: 10.1038/s41438-020-00352-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 05/06/2023]
Abstract
Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.
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Affiliation(s)
- Lin-Feng Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, Arizona USA
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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30
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Walters SJ, Robinson TP, Byrne M, Wardell-Johnson GW, Nevill P. Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species. Mol Ecol 2020; 29:3022-3037. [PMID: 32621768 DOI: 10.1111/mec.15537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022]
Abstract
Sympatric tree species are subject to similar climatic drivers, posing a question as to whether they display comparable adaptive responses. However, no study has explicitly examined local adaptation of co-occurring parasitic and autotrophic plant species to the abiotic environment. Here we test the hypotheses that a generalist parasitic tree would display a weaker signal of selection and that genomic variation would associate with fewer climatic variables (particularly precipitation) but have similar spatial patterns to a sympatric autotrophic tree species. To test these hypotheses, we collected samples from 17 sites across the range of two tree species, the hemiparasite Nuytsia floribunda (n = 264) and sympatric autotroph Melaleuca rhaphiophylla (n = 272). We obtained 5,531 high-quality genome-wide single nucleotide polymorphisms (SNPs) for M. rhaphiophylla and 6,727 SNPs for N. floribunda using DArTseq genome scan technology. Population differentiation and environmental association approaches were used to identify signals of selection. Generalized dissimilarly modelling was used to detect climatic and spatial patterns of local adaptation across climatic gradients. Overall, 322 SNPs were identified as putatively adaptive for the autotroph, while only 57 SNPs were identified for the parasitic species. We found genomic variation to associate with different sets of bioclimatic variables for each species, with precipitation relatively less important for the parasite. Spatial patterns of predicted adaptive variability were different and indicate that co-occurring species with disparate life history traits may not respond equally to selective pressures (i.e., temperature and precipitation). Together, these findings provide insight into local adaptation of sympatric parasitic and autotrophic tree species to abiotic environments.
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Affiliation(s)
- Sheree J Walters
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Todd P Robinson
- School of Earth and Planetary Science, Curtin University, Perth, Western Australia, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Perth, Western Australia, Australia.,School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Grant W Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia.,Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
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31
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Silva AR, Resende-Moreira LC, Carvalho CS, Lanes ECM, Ortiz-Vera MP, Viana PL, Jaffé R. Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas. AOB PLANTS 2020; 12:plaa003. [PMID: 32128104 PMCID: PMC7043808 DOI: 10.1093/aobpla/plaa003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/28/2020] [Indexed: 05/05/2023]
Abstract
Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species' entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (F ST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.
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Affiliation(s)
- Amanda R Silva
- Universidade Federal Rural da Amazônia/Museu Paraense Emílio Goeldi, Programa de Pós-graduação em Ciências Biológicas - Botânica Tropical, Belém-PA, Brazil
- Museu Paraense Emílio Goeldi, Programa de Capacitação Institucional (PCI), Belém-PA, Brazil
| | | | | | - Eder C M Lanes
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
| | - Mabel P Ortiz-Vera
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Genética e Biologia Molecular, Belém-PA, Brazil
| | - Pedro L Viana
- Universidade Federal Rural da Amazônia/Museu Paraense Emílio Goeldi, Programa de Pós-graduação em Ciências Biológicas - Botânica Tropical, Belém-PA, Brazil
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
- Universidade de São Paulo, Departamento de Ecologia, São Paulo-SP, Brazil
- Corresponding author’s email address:
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32
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Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco‐evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large‐scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco‐evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | | | | | - Robert Kofler
- Institute of Population Genetics Vetmeduni Vienna Austria
| | - Thomas Mock
- School of Environmental Sciences University of East Anglia Norwich United Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics University of Hohenheim Stuttgart Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.,Institute of Ecology, Evolution and Diversity Goethe-University Frankfurt am Main Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) Frankfurt am Main Germany
| | | | - Outi Savolainen
- Department of Ecology and Genetics University of Oulu Finland
| | - Alan Bergland
- Department of Biology University of Virginia Charlottesville Virginia
| | - Thomas Flatt
- Department of Biology University of Fribourg Fribourg Switzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) Frankfurt am Main Germany.,Institute for Organismic and Molecular Evolution Johannes Gutenberg University Mainz Germany
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33
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Ahrens CW, Andrew ME, Mazanec RA, Ruthrof KX, Challis A, Hardy G, Byrne M, Tissue DT, Rymer PD. Plant functional traits differ in adaptability and are predicted to be differentially affected by climate change. Ecol Evol 2020; 10:232-248. [PMID: 31988725 PMCID: PMC6972804 DOI: 10.1002/ece3.5890] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/18/2019] [Accepted: 11/10/2019] [Indexed: 12/12/2022] Open
Abstract
Climate change is testing the resilience of forests worldwide pushing physiological tolerance to climatic extremes. Plant functional traits have been shown to be adapted to climate and have evolved patterns of trait correlations (similar patterns of distribution) and coordinations (mechanistic trade-off). We predicted that traits would differentiate between populations associated with climatic gradients, suggestive of adaptive variation, and correlated traits would adapt to future climate scenarios in similar ways.We measured genetically determined trait variation and described patterns of correlation for seven traits: photochemical reflectance index (PRI), normalized difference vegetation index (NDVI), leaf size (LS), specific leaf area (SLA), δ13C (integrated water-use efficiency, WUE), nitrogen concentration (NCONC), and wood density (WD). All measures were conducted in an experimental plantation on 960 trees sourced from 12 populations of a key forest canopy species in southwestern Australia.Significant differences were found between populations for all traits. Narrow-sense heritability was significant for five traits (0.15-0.21), indicating that natural selection can drive differentiation; however, SLA (0.08) and PRI (0.11) were not significantly heritable. Generalized additive models predicted trait values across the landscape for current and future climatic conditions (>90% variance). The percent change differed markedly among traits between current and future predictions (differing as little as 1.5% (δ13C) or as much as 30% (PRI)). Some trait correlations were predicted to break down in the future (SLA:NCONC, δ13C:PRI, and NCONC:WD).Synthesis: Our results suggest that traits have contrasting genotypic patterns and will be subjected to different climate selection pressures, which may lower the working optimum for functional traits. Further, traits are independently associated with different climate factors, indicating that some trait correlations may be disrupted in the future. Genetic constraints and trait correlations may limit the ability for functional traits to adapt to climate change.
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Affiliation(s)
- Collin W. Ahrens
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSWAustralia
| | - Margaret E. Andrew
- Environmental & Conservation SciencesMurdoch UniversityMurdochWAAustralia
| | - Richard A. Mazanec
- Biodiversity and Conservation ScienceWestern Australian Department of Biodiversity, Conservation and AttractionsKensingtonWAAustralia
| | - Katinka X. Ruthrof
- Biodiversity and Conservation ScienceWestern Australian Department of Biodiversity, Conservation and AttractionsKensingtonWAAustralia
- Centre for Phytophthora Science and ManagementEnvironmental & Conservation SciencesMurdoch UniversityMurdochWAAustralia
| | - Anthea Challis
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSWAustralia
| | - Giles Hardy
- Centre for Phytophthora Science and ManagementEnvironmental & Conservation SciencesMurdoch UniversityMurdochWAAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceWestern Australian Department of Biodiversity, Conservation and AttractionsKensingtonWAAustralia
| | - David T. Tissue
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSWAustralia
| | - Paul D. Rymer
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSWAustralia
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34
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Ahrens CW, Mazanec RA, Paap T, Ruthrof KX, Challis A, Hardy G, Byrne M, Tissue DT, Rymer PD. Adaptive variation for growth and resistance to a novel pathogen along climatic gradients in a foundation tree. Evol Appl 2019; 12:1178-1190. [PMID: 31293630 PMCID: PMC6597866 DOI: 10.1111/eva.12796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
Natural ecosystems are under pressure from increasing abiotic and biotic stressors, including climate change and novel pathogens, which are putting species at risk of local extinction, and altering community structure, composition and function. Here, we aim to assess adaptive variation in growth and fungal disease resistance within a foundation tree, Corymbia calophylla to determine local adaptation, trait heritability and genetic constraints in adapting to future environments. Two experimental planting sites were established in regions of contrasting rainfall with seed families from 18 populations capturing a wide range of climate origins (~4,000 individuals at each site). Every individual was measured in 2015 and 2016 for growth (height, basal diameter) and disease resistance to a recently introduced leaf blight pathogen (Quambalaria pitereka). Narrow-sense heritability was estimated along with trait covariation. Trait variation was regressed against climate-of-origin, and multivariate models were used to develop predictive maps of growth and disease resistance. Growth and blight resistance traits differed significantly among populations, and these differences were consistent between experimental sites and sampling years. Growth and blight resistance were heritable, and comparisons between trait differentiation (Q ST) and genetic differentiation (F ST) revealed that population differences in height and blight resistance traits are due to divergent natural selection. Traits were significantly correlated with climate-of-origin, with cool and wet populations showing the highest levels of growth and blight resistance. These results provide evidence that plants have adaptive growth strategies and pathogen defence strategies. Indeed, the presence of standing genetic variation and trait heritability of growth and blight resistance provide capacity to respond to novel, external pressures. The integration of genetic variation into adaptive management strategies, such as assisted gene migration and seed sourcing, may be used to provide greater resilience for natural ecosystems to both biotic and abiotic stressors.
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Affiliation(s)
- Collin W. Ahrens
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Richard A. Mazanec
- Biodiversity and Conservation Science, Bentley Delivery CentreWestern Australian Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Trudy Paap
- Centre for Phytophthora Science and Management, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
- Present address:
Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Katinka X. Ruthrof
- Centre for Phytophthora Science and Management, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
- Kings Park ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Anthea Challis
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Giles Hardy
- Centre for Phytophthora Science and Management, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Bentley Delivery CentreWestern Australian Department of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - David T. Tissue
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Paul D. Rymer
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
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