1
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Feng J, Dan X, Cui Y, Gong Y, Peng M, Sang Y, Ingvarsson PK, Wang J. Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change. PLANT COMMUNICATIONS 2024; 5:101044. [PMID: 39095989 DOI: 10.1016/j.xplc.2024.101044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/03/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024]
Abstract
Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.
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Affiliation(s)
- Jiajun Feng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuming Dan
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yangkai Cui
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Gong
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minyue Peng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yupeng Sang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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2
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Metzger DCH, Earhart ML, Schulte PM. Genomic and Epigenomic Influences on Resilience across Scales: Lessons from the Responses of Fish to Environmental Stressors. Integr Comp Biol 2024; 64:853-866. [PMID: 38632046 PMCID: PMC11445785 DOI: 10.1093/icb/icae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024] Open
Abstract
Understanding the factors that influence the resilience of biological systems to environmental change is a pressing concern in the face of increasing human impacts on ecosystems and the organisms that inhabit them. However, most considerations of biological resilience have focused at the community and ecosystem levels, whereas here we discuss how including consideration of processes occurring at lower levels of biological organization may provide insights into factors that influence resilience at higher levels. Specifically, we explore how processes at the genomic and epigenomic levels may cascade up to influence resilience at higher levels. We ask how the concepts of "resistance," or the capacity of a system to minimize change in response to a disturbance, and "recovery," or the ability of a system to return to its original state following a disturbance and avoid tipping points and resulting regime shifts, map to these lower levels of biological organization. Overall, we suggest that substantial changes at these lower levels may be required to support resilience at higher levels, using selected examples of genomic and epigenomic responses of fish to climate-change-related stressors such as high temperature and hypoxia at the levels of the genome, epigenome, and organism.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Madison L Earhart
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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3
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Ferguson S, Jones A, Murray K, Andrew R, Schwessinger B, Borevitz J. Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence. Genome Res 2024; 34:606-619. [PMID: 38589251 PMCID: PMC11146599 DOI: 10.1101/gr.277999.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence, genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and the subsequent divergence beyond recognition of rearrangements become the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence but at a slower pace than that of rearrangements. We hypothesize that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- Weigel Department, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Rose Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
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4
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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5
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Ferguson S, Jones A, Murray K, Andrew RL, Schwessinger B, Bothwell H, Borevitz J. Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus. Gigascience 2024; 13:giae029. [PMID: 38869149 PMCID: PMC11170218 DOI: 10.1093/gigascience/giae029] [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: 11/05/2023] [Revised: 03/11/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Structural variations (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of Eucalyptus melliodora and Eucalyptus sideroxylon, along with recent high-quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads in E. melliodora and E. sideroxylon, respectively. Focusing on inversions and translocations, symmetric SVs that are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076 Germany
| | - Rose L Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Helen Bothwell
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens 30602 GA, United States
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
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6
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Hung TH, So T, Thammavong B, Chamchumroon V, Theilade I, Phourin C, Bouamanivong S, Hartvig I, Gaisberger H, Jalonen R, Boshier DH, MacKay JJ. Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods. Proc Natl Acad Sci U S A 2023; 120:e2301603120. [PMID: 37549265 PMCID: PMC10438386 DOI: 10.1073/pnas.2301603120] [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: 01/29/2023] [Accepted: 06/15/2023] [Indexed: 08/09/2023] Open
Abstract
In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.
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Affiliation(s)
- Tin Hang Hung
- Department of Biology, University of Oxford, OxfordOX1 3RB, United Kingdom
| | - Thea So
- Institute of Forest and Wildlife Research and Development, Phnom Penh, Cambodia
| | - Bansa Thammavong
- National Agriculture and Forestry Research Institute, Forestry Research Center, Vientiane, Laos
| | - Voradol Chamchumroon
- The Forest Herbarium, Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok10900, Thailand
| | - Ida Theilade
- Department of Food and Resource Economics, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958Frederiksberg C, Denmark
| | - Chhang Phourin
- Institute of Forest and Wildlife Research and Development, Phnom Penh, Cambodia
| | - Somsanith Bouamanivong
- National Herbarium of Laos, Biotechnology and Ecology Institute, Ministry of Science and Technology, Vientiane, Laos
| | - Ida Hartvig
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958Frederiksberg C, Denmark
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Hannes Gaisberger
- Bioversity International, I-00057Rome, Italy
- Department of Geoinformatics, Paris Lodron University, 5020Salzburg, Austria
| | | | - David H. Boshier
- Department of Biology, University of Oxford, OxfordOX1 3RB, United Kingdom
| | - John J. MacKay
- Department of Biology, University of Oxford, OxfordOX1 3RB, United Kingdom
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7
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Rosser NL, Quinton A, Davey H, Ayre DJ, Denham AJ. Genetic assessment of the value of restoration planting within an endangered eucalypt woodland. Sci Rep 2023; 13:6583. [PMID: 37085553 PMCID: PMC10121665 DOI: 10.1038/s41598-023-33720-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 04/18/2023] [Indexed: 04/23/2023] Open
Abstract
Assessment of woodland restoration often focusses on stand demographics, but genetic factors likely influence long-term stand viability. We examined the genetic composition of Yellow Box (Eucalyptus melliodora) trees in endangered Box-Gum Grassy Woodland in SE Australia, some 30 years after planting with seeds of reportedly local provenance. Using DArT sequencing for 1406 SNPs, we compared genetic diversity and population structure of planted E. melliodora trees with remnant bushland trees, paddock trees and natural recruits. Genetic patterns imply that natural stands and paddock trees had historically high gene flow (among group pairwise FST = 0.04-0.10). Genetic diversity was highest among relictual paddock trees (He = 0.17), while diversity of revegetated trees was identical to natural bushland trees (He = 0.14). Bayesian clustering placed the revegetated trees into six genetic groups with four corresponding to genotypes from paddock trees, indicating that revegetated stands are mainly of genetically diverse, local provenance. Natural recruits were largely derived from paddock trees with some contribution from planted trees. A few trees have likely hybridised with other local eucalypt species which are unlikely to compromise stand integrity. We show that paddock trees have high genetic diversity and capture historic genetic variety and provide important foci for natural recruitment of genetically diverse and outcrossed seedlings.
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Affiliation(s)
- Natalie L Rosser
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Anthony Quinton
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Huw Davey
- Independent Researcher, Wollongong, NSW, Australia
| | - David J Ayre
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Andrew J Denham
- Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia.
- Science, Economics and Insights Division, NSW Department of Planning and Environment, Parramatta, NSW, Australia.
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8
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Putra AR, Yen JDL, Fournier-Level A. Forecasting trait responses in novel environments to aid seed provenancing under climate change. Mol Ecol Resour 2023; 23:565-580. [PMID: 36308465 DOI: 10.1111/1755-0998.13728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/28/2022]
Abstract
Revegetation projects face the major challenge of sourcing optimal plant material. This is often done with limited information about plant performance and increasingly requires factoring resilience to climate change. Functional traits can be used as quantitative indices of plant performance and guide seed provenancing, but trait values expected under novel conditions are often unknown. To support climate-resilient provenancing efforts, we develop a trait prediction model that integrates the effect of genetic variation with fine-scale temperature variation. We train our model on multiple field plantings of Arabidopsis thaliana and predict two relevant fitness traits-days-to-bolting and fecundity-across the species' European range. Prediction accuracy was high for days-to-bolting and moderate for fecundity, with the majority of trait variation explained by temperature differences between plantings. Projection under future climate predicted a decline in fecundity, although this response was heterogeneous across the range. In response, we identified novel genotypes that could be introduced to genetically offset the fitness decay. Our study highlights the value of predictive models to aid seed provenancing and improve the success of revegetation projects.
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Affiliation(s)
- Andhika R Putra
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jian D L Yen
- Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
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9
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Zhang X, Guo R, Shen R, Landis JB, Jiang Q, Liu F, Wang H, Yao X. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. HORTICULTURE RESEARCH 2023; 10:uhad031. [PMID: 37799629 PMCID: PMC10548413 DOI: 10.1093/hr/uhad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/14/2023] [Indexed: 10/07/2023]
Abstract
A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in the southern tropical region of China, occurring in spatially heterogeneous environments. In the present study we combined population genomic, epigenomic, and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient, and to assess genomic offset to climatic change for A. eriantha. The population structure is strongly shaped by geography and influenced by restricted gene flow resulting from isolation by distance due to habitat fragmentation. In total, we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation, which were enriched in functional categories related to development processes and stress response; both temperature and precipitation are important factors driving adaptive variation. In addition to single-nucleotide polymorphisms (SNPs), a total of 27 single-methylation variants (SMVs) had significant correlation with at least one of four climatic variables and 16 SMVs were located in or adjacent to genes, several of which were predicted to be involved in plant response to abiotic or biotic stress. Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change. Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation. Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruinan Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853 USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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10
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Exposito-Alonso M. Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology. THE NEW PHYTOLOGIST 2023; 237:2005-2011. [PMID: 36604850 DOI: 10.1111/nph.18718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because different populations may be more or less susceptible to global change and, if lost, would reduce the total diversity within a species. Two new modeling frameworks advance our understanding of extinction from a population and evolutionary angle: Rapid climate change-driven disruptions in population adaptation are predicted from associations between genomes and local climates. Furthermore, losses of population diversity from global land-use transformations are estimated by scaling relationships of species' genomic diversity with habitat area. Overall, these global eco-evolutionary methods advance the predictability - and possibly the preventability - of the ongoing extinction of plant species.
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Affiliation(s)
- Moi Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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11
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Ferguson S, Jones A, Murray K, Schwessinger B, Borevitz JO. Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus. Mol Ecol 2023; 32:1271-1287. [PMID: 35810343 DOI: 10.1111/mec.16608] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022]
Abstract
Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long-read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small-scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.,Weigel Department, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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12
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Alaniz AJ, Smith-Ramírez C, Rendón-Funes A, Hidalgo-Corrotea C, Carvajal MA, Vergara PM, Fuentes N. Multiscale spatial analysis of headwater vulnerability in South-Central Chile reveals a high threat due to deforestation and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157930. [PMID: 35952895 DOI: 10.1016/j.scitotenv.2022.157930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Headwaters represent an essential component of hydrological, ecological, and socioeconomical systems, by providing constant water streams to the complete basin. However, despite the high importance of headwaters, there is a lack of vulnerability assessments worldwide. Identifying headwaters and their vulnerability in a spatially explicit manner can enable restauration and conservation programs. In this study, we assess the vulnerability of headwaters in South-Central Chile (38.4 to 43.2°S) considering multiple degradation factors related to climate change and land cover change. We analyzed 2292 headwaters, characterizing multiple factors at five spatial scales by using remote sensing data related to Land Use and Cover Change (LUCC), human disturbances, vegetation cover, climate change, potential water demand, and physiography. We then generated an index of vulnerability by integrating all the analyzed variables, which allowed us to map the spatial distribution of headwater vulnerability. Finally, to estimate the main drivers of degradation, we performed a Principal Components Analysis with an Agglomerative Hierarchical Clustering, that allowed us to group headwaters according to the analyzed factors. The largest proportion of most vulnerable headwaters are located in the north of our study area with 48.1 %, 62.1 %, and 28.1 % of headwaters classified as highly vulnerable at 0, 10, and 30 m scale, respectively. The largest proportion of headwaters are affected by Climate Change (63.66 %) and LUCC (23.02 %) on average across all scales. However, we identified three clusters, in which the northern cluster is mainly affected by LUCC, while the Andean and Coastal clusters are mainly affected by climate change. Our results and methods present an informative picture of the current state of headwater vulnerability, identifying spatial patterns and drivers at multiple scales. We believe that the approach developed in this study could be useful for new studies in other zones of the world and can also promote Chilean headwater conservation.
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Affiliation(s)
- Alberto J Alaniz
- Departamento de Ingeniería Geográfica, Facultad de Ingeniería, Universidad de Santiago de Chile, Chile; Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Cecilia Smith-Ramírez
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, 1305 Av. Fuchslocher, Osorno, Chile; Instituto de Ecología y Biodiversidad-Chile (IEB), Las Palmeras 3425, Santiago, Chile; Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Isla Teja s/n, Valdivia, Chile
| | - Adriana Rendón-Funes
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, 1305 Av. Fuchslocher, Osorno, Chile; Instituto de Ecología y Biodiversidad-Chile (IEB), Las Palmeras 3425, Santiago, Chile; Área de Ecología, Museo de Historia Natural Alcide d'Orbigny, 1458 Av. Potosí, Cochabamba, Bolivia
| | | | - Mario A Carvajal
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Gestión Agraria, Facultad Tecnológica, Universidad de Santiago de Chile, Chile
| | - Pablo M Vergara
- Departamento de Gestión Agraria, Facultad Tecnológica, Universidad de Santiago de Chile, Chile
| | - Norka Fuentes
- Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Av. Fuchslocher 1305, Osorno, Chile
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13
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Fahey PS, Udovicic F, Cantrill DJ, Bayly MJ. A box on the river: The phylogenetics and phylogeography of Eucalyptus baueriana (Eucalyptus sect. Adnataria ser. Heterophloiae). PLoS One 2022; 17:e0276117. [PMID: 36395183 PMCID: PMC9671351 DOI: 10.1371/journal.pone.0276117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
We present a phylogeographic study of the tree species Eucalyptus baueriana Schauer, which occurs in disjunct areas on the near coastal plains and ranges of the south-east Australian mainland. DArTseq data are used to build a phylogeny including E. baueriana and closely related taxa to test its monophyly, test the genetic distinctness of the three subspecies of E. baueriana, and investigate relationships between its disjunct populations. Additionally, we use population structure analysis to investigate the genetic distinctness of populations, and MaxEnt to investigate the environmental factors potentially influencing the species' distribution. We show E. baueriana is monophyletic and most closely related to three other Blue Box eucalypt species: E. conica H.Deane & Maiden, E. dalveenica T.L.Collins, R.L.Andrew & J.J.Bruhl and E. magnificata L.A.S.Johnson & K.D.Hill, with some evidence for genetic introgression between these taxa. Within E. baueriana, the deepest genetic breaks do not correspond with the subspecies classification as the two geographically restricted subspecies, together with samples of the more widespread E. baueriana subsp. baueriana from west of the Gippsland lowlands, form a south-western clade with that is sister to other populations of subsp. baueriana. The oldest genetic break in the species occurs in far eastern Gippsland (Victoria), corresponding to one of the shortest geographic disjunctions in the species' distribution. Genetic breaks in other species have been observed in this region which is broadly referred to as the southern transition zone. Both total annual rainfall and the seasonality of this rainfall are hypothesised to affect the species' distribution; gaps in its distribution are in areas of higher rainfall that support closed forest and in regions with more winter dominated rainfall.
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Affiliation(s)
- Patrick S. Fahey
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Frank Udovicic
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | | | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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14
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Exposito-Alonso M, Booker TR, Czech L, Gillespie L, Hateley S, Kyriazis CC, Lang PLM, Leventhal L, Nogues-Bravo D, Pagowski V, Ruffley M, Spence JP, Toro Arana SE, Weiß CL, Zess E. Genetic diversity loss in the Anthropocene. Science 2022; 377:1431-1435. [PMID: 36137047 DOI: 10.1126/science.abn5642] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Anthropogenic habitat loss and climate change are reducing species' geographic ranges, increasing extinction risk and losses of species' genetic diversity. Although preserving genetic diversity is key to maintaining species' adaptability, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. We introduce a mathematical framework that bridges biodiversity theory and population genetics to understand the loss of naturally occurring DNA mutations with decreasing habitat. By analyzing genomic variation of 10,095 georeferenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a mutations-area relationship power law with geographic area, which can predict genetic diversity loss from local population extinctions. We estimate that more than 10% of genetic diversity may already be lost for many threatened and nonthreatened species, surpassing the United Nations' post-2020 targets for genetic preservation.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Lauren Gillespie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | | | - Laura Leventhal
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Nogues-Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Megan Ruffley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Jeffrey P Spence
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sebastian E Toro Arana
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin Zess
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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15
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Walters SJ, Robinson TP, Byrne M, Nevill P. Seed sourcing in the genomics era: Multispecies provenance delineation for current and future climates. Restor Ecol 2022. [DOI: 10.1111/rec.13718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheree J. Walters
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences Curtin University Bentley WA 6102 Australia
| | - Todd P. Robinson
- School of Earth and Planetary Sciences Curtin University Bentley WA 6102 Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre WA 6983 Australia
- School of Molecular and Life Sciences Curtin University Bentley WA 6102 Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences Curtin University Bentley WA 6102 Australia
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences Curtin University Bentley WA 6102 Australia
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16
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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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17
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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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18
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Westergaard KB, Kyrkjeeide MO, Brandrud MK. Using genomics to guide seed-sourcing at the right taxonomical level for ecological restoration projects: The complex case of Carex bigelowii s.lat. in Norway. Ecol Evol 2021; 11:17117-17131. [PMID: 34938497 PMCID: PMC8668773 DOI: 10.1002/ece3.8350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
There is a growing demand for ecological restoration using suitable seeds following international standards or national legal demands for local seed-sourcing. However, before selecting the appropriate geographic origin of seeds, it is vital to explore taxonomic complexity related to the focal taxa. We used ddRAD-seq to screen genomic diversity within Carex bigelowii s.lat. focussing on Norway. This species complex is considered a candidate for seeding, but presents considerable morphological, ecological, and genetic variation. The genetic structure of 132 individuals of C. bigelowii s.lat., including Carex nigra as an outgroup, was explored using ordinations, clustering analyses, and a genetic barrier algorithm. Two highly divergent clusters were evident, supporting the recognition of two taxonomic units "C. dacica" and C. bigelowii "subsp. bigelowii". Previously defined seed-sourcing regions for C. bigelowii s.lat. did not consider the known taxonomic complexity, and therefore interpreted the overall genetic structure as seed-sourcing regions, not taxa. We estimated genetic neighborhood sizes within each taxon to be 100-150 km and 300 km, respectively, indicating species-specific delimitations of local seed-sourcing regions. Frequent hybrids, local genetic distinctiveness, and suggested ecotypes add complexity to the discussed seed-sourcing regions. Our results show how genomic screening of diversity and structure in a species complex can alleviate the taxonomic impediment, inform practical questions, and legal requirements related to seed-sourcing, and together with traditional taxonomic work provide necessary information for a sound management of biodiversity.
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19
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Patturaj M, Munusamy A, Kannan N, Kandasamy U, Ramasamy Y. Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation. Genomics Inform 2021; 19:e33. [PMID: 34638180 PMCID: PMC8510864 DOI: 10.5808/gi.21031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022] Open
Abstract
Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%–62.5%), followed by tri- (23.7%–27.2%), tetra- (5.2%–5.6%), penta- (5.0%–5.3%), and hexa-nucleotide (2.7%–2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.
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Affiliation(s)
- Maheswari Patturaj
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
| | - Aiswarya Munusamy
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
| | | | | | - Yasodha Ramasamy
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
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20
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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21
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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22
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Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
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23
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Vanhove M, Pina‐Martins F, Coelho AC, Branquinho C, Costa A, Batista D, Príncipe A, Sousa P, Henriques A, Marques I, Belkadi B, Knowles LL, Paulo OS. Using gradient Forest to predict climate response and adaptation in Cork oak. J Evol Biol 2021; 34:910-923. [DOI: 10.1111/jeb.13765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Mathieu Vanhove
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Francisco Pina‐Martins
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Ana Cristina Coelho
- Centro de Electrónica, Optoelectronica e Telecomunicações Universidade do Algarve Faro Portugal
| | - Cristina Branquinho
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária Oeiras Portugal
- CENSE ‐ Center for Environmental and Sustainability Research NOVA University of Lisbon Caparica Portugal
| | - Dora Batista
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | - Adriana Príncipe
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Paulo Sousa
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - André Henriques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Isabel Marques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Forest Research Centre Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | | | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Octávio S. Paulo
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
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24
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Coleman MA, Bragg JG. A decision framework for evidence-based climate adaptation interventions. GLOBAL CHANGE BIOLOGY 2021; 27:472-474. [PMID: 33128838 DOI: 10.1111/gcb.15429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Climate change is outpacing the ability of species and populations to naturally adapt warranting active interventions to boost climate resilience. In their review paper, Gaitán-Espitia and Hobday discuss how such interventions may, however, counter natural evolutionary processes and adaptive capacity if not underpinned by background knowledge from genes through to ecosystems. They present a robust decision framework to guide implementation of climate adaptation interventions to avoid unintended evolutionary outcomes.
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Affiliation(s)
- Melinda A Coleman
- New South Wales Fisheries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- Southern Cross University, National Marine Science Centre, Coffs Harbour, NSW, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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25
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Fahey PS, Fowler RM, McLay TGB, Udovicic F, Cantrill DJ, Bayly MJ. Divergent lineages in a semi-arid mallee species, Eucalyptus behriana, correspond to a major geographic break in southeastern Australia. Ecol Evol 2021; 11:664-678. [PMID: 33437459 PMCID: PMC7790638 DOI: 10.1002/ece3.7099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 12/02/2022] Open
Abstract
AIM To infer relationships between populations of the semi-arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia. LOCATION Southeastern Australia. TAXON Eucalyptus behriana (Myrtaceae, Angiospermae). METHODS We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site-associated DNA sequencing (ddRAD-seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species' distribution. RESULTS Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them. CONCLUSIONS Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial-interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role.
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Affiliation(s)
- Patrick S. Fahey
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
| | - Rachael M. Fowler
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
| | - Todd G. B. McLay
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
- Royal Botanic Gardens VictoriaSouth YarraVic.Australia
| | | | | | - Michael J. Bayly
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
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26
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Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-020720-042553] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland 21532, USA
| | - Rachael A. Bay
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
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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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Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species. DIVERSITY 2020. [DOI: 10.3390/d12080306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.
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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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Carvalho CS, Forester BR, Mitre SK, Alves R, Imperatriz-Fonseca VL, Ramos SJ, Resende-Moreira LC, Siqueira JO, Trevelin LC, Caldeira CF, Gastauer M, Jaffé R. Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration. Mol Ecol Resour 2020; 21:44-58. [PMID: 32419278 DOI: 10.1111/1755-0998.13191] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Despite the importance of climate-adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron-rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype-phenotype-environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site-adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.
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Affiliation(s)
- Carolina S Carvalho
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | - José O Siqueira
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | | | | | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Departamento de Ecologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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32
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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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33
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Ingvarsson PK, Bernhardsson C. Genome-wide signatures of environmental adaptation in European aspen ( Populus tremula) under current and future climate conditions. Evol Appl 2020; 13:132-142. [PMID: 31892948 PMCID: PMC6935590 DOI: 10.1111/eva.12792] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 12/30/2022] Open
Abstract
Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess local adaptation to current climate in European aspen (Populus tremula) by using environmental association analyses to identify genetic variants associated with two representative climate variables describing current day variation in temperature and precipitation. We also analysed patterns of genetic differentiation between southern and northern populations and observe that regions of high genetic differentiation are enriched for SNPs that are significantly associated with climate. Using variants associated with climate, we examined patterns of isolation by distance and environment and used spatial modelling to predict the geographic distribution of genomic variation in response to two scenarios of future climate change. We show that climate conditions at a northern reference site will correspond to climate conditions experienced by current day populations located 4-8 latitude degrees further south. By assessing the relationship between phenotypic traits and vegetative fitness, we also demonstrate that southern populations harbour genetic variation that likely would be adaptive further north under both climate change scenarios. Current day populations at the lagging edge of the distribution in Sweden can therefore serve as sources for introducing adaptive alleles onto northern populations, but the likelihood of this largely depends on naturally occurring levels of gene flow.
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Affiliation(s)
- Pär K. Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant BiologySwedish University of Agricultural SciencesUppsalaSweden
| | - Carolina Bernhardsson
- Department of Plant Biology, Linnean Centre for Plant BiologySwedish University of Agricultural SciencesUppsalaSweden
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
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34
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Cooke SJ, Madliger CL, Cramp RL, Beardall J, Burness G, Chown SL, Clark TD, Dantzer B, de la Barrera E, Fangue NA, Franklin CE, Fuller A, Hawkes LA, Hultine KR, Hunt KE, Love OP, MacMillan HA, Mandelman JW, Mark FC, Martin LB, Newman AEM, Nicotra AB, Robinson SA, Ropert-Coudert Y, Rummer JL, Seebacher F, Todgham AE. Reframing conservation physiology to be more inclusive, integrative, relevant and forward-looking: reflections and a horizon scan. CONSERVATION PHYSIOLOGY 2020; 8:coaa016. [PMID: 32274063 PMCID: PMC7125050 DOI: 10.1093/conphys/coaa016] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 05/21/2023]
Abstract
Applying physiological tools, knowledge and concepts to understand conservation problems (i.e. conservation physiology) has become commonplace and confers an ability to understand mechanistic processes, develop predictive models and identify cause-and-effect relationships. Conservation physiology is making contributions to conservation solutions; the number of 'success stories' is growing, but there remain unexplored opportunities for which conservation physiology shows immense promise and has the potential to contribute to major advances in protecting and restoring biodiversity. Here, we consider how conservation physiology has evolved with a focus on reframing the discipline to be more inclusive and integrative. Using a 'horizon scan', we further explore ways in which conservation physiology can be more relevant to pressing conservation issues of today (e.g. addressing the Sustainable Development Goals; delivering science to support the UN Decade on Ecosystem Restoration), as well as more forward-looking to inform emerging issues and policies for tomorrow. Our horizon scan provides evidence that, as the discipline of conservation physiology continues to mature, it provides a wealth of opportunities to promote integration, inclusivity and forward-thinking goals that contribute to achieving conservation gains. To advance environmental management and ecosystem restoration, we need to ensure that the underlying science (such as that generated by conservation physiology) is relevant with accompanying messaging that is straightforward and accessible to end users.
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Affiliation(s)
- Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Dr., Ottawa, ON, K1S 5B6, Canada
- Corresponding author: Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Dr., Ottawa, ON, K1S 5B6, Canada.
| | - Christine L Madliger
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, 1125 Colonel By Dr., Ottawa, ON, K1S 5B6, Canada
| | - Rebecca L Cramp
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Gary Burness
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Timothy D Clark
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 14 3216, Australia
| | - Ben Dantzer
- Department of Psychology, Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erick de la Barrera
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Morelia, Michoacán, 58190, Mexico
| | - Nann A Fangue
- Department of Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Craig E Franklin
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Andrea Fuller
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, 7 York Rd, Parktown, 2193, South Africa
| | - Lucy A Hawkes
- College of Life and Environmental Sciences, Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA
| | - Kathleen E Hunt
- Department of Biology, George Mason University, Fairfax, VA 22030, USA
| | - Oliver P Love
- Department of Integrative Biology, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Heath A MacMillan
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - John W Mandelman
- Anderson Cabot Center for Ocean Life, New England Aquarium, 1 Central Wharf, Boston, MA 02110, USA
| | - Felix C Mark
- Department of Integrative Ecophysiology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27574 Bremerhaven, Germany
| | - Lynn B Martin
- Global Health and Infectious Disease Research, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL 33612, USA
| | - Amy E M Newman
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Adrienne B Nicotra
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Sharon A Robinson
- School of Earth, Atmospheric and Life Sciences (SEALS) and Centre for Sustainable Ecosystem Solutions, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yan Ropert-Coudert
- Centre d'Etudes Biologiques de Chizé, CNRS UMR 7372 - La Rochelle Université, 79360 Villiers-en-Bois, France
| | - Jodie L Rummer
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 5811, Australia
| | - Frank Seebacher
- School of Life and Environmental Sciences A08, University of Sydney, NSW 2006, Australia
| | - Anne E Todgham
- Department of Animal Science, University of California Davis, One Shields Ave. Davis, CA, 95616, USA
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Murray KD, Janes JK, Jones A, Bothwell HM, Andrew RL, Borevitz JO. Landscape drivers of genomic diversity and divergence in woodland Eucalyptus. Mol Ecol 2019; 28:5232-5247. [PMID: 31647597 PMCID: PMC7065176 DOI: 10.1111/mec.15287] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/23/2019] [Indexed: 01/03/2023]
Abstract
Spatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L'Héritier 1789; the "eucalypts") are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole-genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity (π ≈ 0.05) and low genome-wide, interspecific differentiation (FST = 0.15) and intraspecific differentiation between localities (FST ≈ 0.01-0.02). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalized dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e. IBE). Eucalyptus sideroxylon showed much stronger IBD and moderate IBE. These results highlight the vast adaptive potential of these species and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.
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Affiliation(s)
| | - Jasmine K Janes
- University of New EnglandArmidaleNSWAustralia
- Vancouver Island University,NanaimoBCCanada
| | - Ashley Jones
- Australian National UniversityCanberraACTAustralia
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Breed MF, Harrison PA, Blyth C, Byrne M, Gaget V, Gellie NJC, Groom SVC, Hodgson R, Mills JG, Prowse TAA, Steane DA, Mohr JJ. The potential of genomics for restoring ecosystems and biodiversity. Nat Rev Genet 2019; 20:615-628. [PMID: 31300751 DOI: 10.1038/s41576-019-0152-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 01/12/2023]
Abstract
Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.
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Affiliation(s)
- Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.
| | - Peter A Harrison
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Colette Blyth
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Western Australia, Australia
| | - Virginie Gaget
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Scott V C Groom
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Riley Hodgson
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Thomas A A Prowse
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.,School of Mathematical Sciences, University of Adelaide, North Terrace, South Australia, Australia
| | - Dorothy A Steane
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Jakki J Mohr
- College of Business, Institute on Ecosystems, University of Montana, Missoula, MT, USA
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37
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von Takach Dukai B, Jack C, Borevitz J, Lindenmayer DB, Banks SC. Pervasive admixture between eucalypt species has consequences for conservation and assisted migration. Evol Appl 2019; 12:845-860. [PMID: 30976314 PMCID: PMC6439489 DOI: 10.1111/eva.12761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/05/2018] [Accepted: 12/21/2018] [Indexed: 01/12/2023] Open
Abstract
Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south-eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.
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Affiliation(s)
- Brenton von Takach Dukai
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Cameron Jack
- ANU Bioinformatics Consultancy, John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Justin Borevitz
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
- Centre of Excellence in Plant Energy BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - David B. Lindenmayer
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Sam C. Banks
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthwest TerritoriesAustralia
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Rossetto M, Bragg J, Kilian A, McPherson H, van der Merwe M, Wilson PD. Restore and Renew: a genomics‐era framework for species provenance delimitation. Restor Ecol 2018. [DOI: 10.1111/rec.12898] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Maurizio Rossetto
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Jason Bragg
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Andrzej Kilian
- Diversity Arrays TechnologyUniversity of Canberra Bruce ACT 2617 Australia
| | - Hannah McPherson
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Marlien van der Merwe
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
| | - Peter D. Wilson
- National Herbarium of New South WalesRoyal Botanic Garden Sydney Mrs Macquaries Road, Sydney NSW 2000 Australia
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