1
|
Aitken SN, Jordan R, Tumas HR. Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:707-736. [PMID: 38594931 DOI: 10.1146/annurev-arplant-070523-044239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.
Collapse
Affiliation(s)
- Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| | | | - Hayley R Tumas
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| |
Collapse
|
2
|
Prakash A, Capblancq T, Shallows K, Saville D, Landau D, Landress C, Jacobs T, Keller S. Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11600. [PMID: 38912128 PMCID: PMC11192164 DOI: 10.1002/aps3.11600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 06/25/2024]
Abstract
Premise Global anthropogenic change threatens the health and productivity of forest ecosystems. Assisted migration and reforestation are tools to help mitigate these impacts. However, questions remain about how to approach sourcing seeds to ensure high establishment and future adaptability. Methods Using exome-capture sequencing, we demonstrate a computational approach to finding the best n-sets from a candidate list of seed sources that collectively achieve high genetic diversity (GD) and minimal genetic load (GL), while also increasing evolvability in quantitative traits. The benefits of this three-part strategy (diversity-load-evolvability) are to increase near-term establishment success while also boosting evolutionary potential to respond to future stressors. Members of The Nature Conservancy and the Central Appalachian Spruce Restoration Initiative planted 58,000 seedlings across 255 acres. A subset of seedlings was monitored for establishment success and variation in growth. Results The results show gains in GD relative to GL and increases in quantitative genetic variation in seedling growth for pooled vs. single-source restoration. No single "super source" was observed across planting sites; rather, monitoring results demonstrate that pooling of multiple sources helps achieve higher GD:GL and evolvability. Discussion Our study shows the potential for integrating genomics into local-scale restoration and the importance of building partnerships between academic researchers and applied conservation managers.
Collapse
Affiliation(s)
- Anoob Prakash
- Department of Plant BiologyUniversity of VermontBurlingtonVermontUSA
| | - Thibaut Capblancq
- Department of Plant BiologyUniversity of VermontBurlingtonVermontUSA
- Laboratoire d'Écologie Alpine, Université Grenoble‐Alpes, Université Savoie Mont Blanc, CNRSGrenobleFrance
| | - Kathryn Shallows
- Central Appalachians Program, The Nature ConservancyElkinsWest VirginiaUSA
| | - David Saville
- Appalachian Forest Restoration LLCMorgantownWest VirginiaUSA
| | - Deborah Landau
- Maryland/DC Chapter, The Nature ConservancyBethesdaMarylandUSA
| | - Chad Landress
- USDA Forest Service, Monongahela National ForestElkinsWest VirginiaUSA
| | - Tal Jacobs
- Clinch Valley Program, The Nature ConservancyAbingdonVirginiaUSA
| | - Stephen Keller
- Department of Plant BiologyUniversity of VermontBurlingtonVermontUSA
| |
Collapse
|
3
|
Vilà-Cabrera A, Astigarraga J, Jump AS, Zavala MA, Seijo F, Sperlich D, Ruiz-Benito P. Anthropogenic land-use legacies underpin climate change-related risks to forest ecosystems. TRENDS IN PLANT SCIENCE 2023; 28:1132-1143. [PMID: 37263916 DOI: 10.1016/j.tplants.2023.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/13/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
Forest ecosystems with long-lasting human imprints can emerge worldwide as outcomes of land-use cessation. However, the interaction of these anthropogenic legacies with climate change impacts on forests is not well understood. Here, we set out how anthropogenic land-use legacies that persist in forest properties, following alterations in forest distribution, structure, and composition, can interact with climate change stressors. We propose a risk-based framework to identify anthropogenic legacies of land uses in forest ecosystems and quantify the impact of their interaction with climate-related stress on forest responses. Considering anthropogenic land-use legacies alongside environmental drivers of forest ecosystem dynamics will improve our predictive capacity of climate-related risks to forests and our ability to promote ecosystem resilience to climate change.
Collapse
Affiliation(s)
- Albert Vilà-Cabrera
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain; Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK; Universidad de Alcalá, Grupo de Ecología y Restauración Forestal, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain.
| | - Julen Astigarraga
- Universidad de Alcalá, Grupo de Ecología y Restauración Forestal, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain
| | - Alistair S Jump
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Miguel A Zavala
- Universidad de Alcalá, Grupo de Ecología y Restauración Forestal, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain
| | - Francisco Seijo
- Instituto de Empresa, School of Global and Public Affairs, Madrid, Spain
| | - Dominik Sperlich
- Department of Forestry Economics and Forest Planning, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Paloma Ruiz-Benito
- Universidad de Alcalá, Grupo de Ecología y Restauración Forestal, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain; Universidad de Alcalá, Grupo de Investigación en Teledetección Ambiental, Departamento de Geología, Geografía y Medio Ambiente, 28801 Alcalá de Henares, Madrid, Spain
| |
Collapse
|
4
|
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] [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.
Collapse
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.
| |
Collapse
|
5
|
Multiplexed ISSR Genotyping by Sequencing (MIG-Seq). Methods Mol Biol 2023; 2638:403-414. [PMID: 36781659 DOI: 10.1007/978-1-0716-3024-2_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.
Collapse
|
6
|
Wagatsuma S, Imanishi J, Suyama Y, Matsuo A, Sato MP, Mitsuyuki C, Tsunamoto Y, Tominaga T, Shimono Y. Revegetation in Japan overlooks geographical genetic structure of native
Artemisia indica
var.
maximowiczii
populations. Restor Ecol 2022. [DOI: 10.1111/rec.13567] [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)
- Satoshi Wagatsuma
- Graduate School of Agriculture Kyoto University, Kitashirakawa Oiwake‐cho, Sakyo‐ku Kyoto 606‐8502 Japan
| | - Junichi Imanishi
- Graduate School of Life and Environmental Sciences Osaka Prefecture University, 1‐1, Gakuen‐cho, Naka‐ku, Sakai Osaka 599‐8531 Japan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science Tohoku University, 232‐3, Yomogida, Naruko‐onsen, Osaki Miyagi 989‐6711 Japan
| | - Ayumi Matsuo
- Graduate School of Agricultural Science Tohoku University, 232‐3, Yomogida, Naruko‐onsen, Osaki Miyagi 989‐6711 Japan
| | - Mitsuhiko P. Sato
- Graduate School of Agricultural Science Tohoku University, 232‐3, Yomogida, Naruko‐onsen, Osaki Miyagi 989‐6711 Japan
| | - Chika Mitsuyuki
- Graduate School of Agricultural Science Tohoku University, 232‐3, Yomogida, Naruko‐onsen, Osaki Miyagi 989‐6711 Japan
| | - Yoshihiro Tsunamoto
- Graduate School of Agricultural Science Tohoku University, 232‐3, Yomogida, Naruko‐onsen, Osaki Miyagi 989‐6711 Japan
| | - Tohru Tominaga
- Graduate School of Agriculture Kyoto University, Kitashirakawa Oiwake‐cho, Sakyo‐ku Kyoto 606‐8502 Japan
| | - Yoshiko Shimono
- Graduate School of Agriculture Kyoto University, Kitashirakawa Oiwake‐cho, Sakyo‐ku Kyoto 606‐8502 Japan
| |
Collapse
|
7
|
Hoban S, Archer FI, Bertola LD, Bragg JG, Breed MF, Bruford MW, Coleman MA, Ekblom R, Funk WC, Grueber CE, Hand BK, Jaffé R, Jensen E, Johnson JS, Kershaw F, Liggins L, MacDonald AJ, Mergeay J, Miller JM, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter KM, Razgour O, Vernesi C, Hunter ME. Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biol Rev Camb Philos Soc 2022; 97:1511-1538. [PMID: 35415952 PMCID: PMC9545166 DOI: 10.1111/brv.12852] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
Abstract
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
Collapse
Affiliation(s)
- Sean Hoban
- Center for Tree Science, The Morton Arboretum, 4100 Illinois Rt 53, Lisle, IL, 60532, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, NOAA/NMFS, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Laura D Bertola
- City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, University Drive, Bedford Park, SA, 5042, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
| | - Melinda A Coleman
- Department of Primary Industries, New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Blekholmsterrassen 36, Stockholm, SE-106 48, Sweden
| | - W Chris Funk
- Department of Biology, Graduate Degree in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523-1878, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Carslaw Building, Sydney, NSW, 2006, Australia
| | - Brian K Hand
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Rodolfo Jaffé
- Exponent, 15375 SE 30th Place, Suite 250, Bellevue, WA, 98007, USA
| | - Evelyn Jensen
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, Newcastle Upon Tyne, NE1 7RU, UK
| | - Jeremy S Johnson
- Department of Environmental Studies, Prescott College, 220 Grove Avenue, Prescott, AZ, 86303, USA
| | - Francine Kershaw
- Natural Resources Defense Council, 40 West 20th Street, New York, NY, 10011, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Ōtehā Rohe campus, Gate 4 Albany Highway, Auckland, Aotearoa, 0745, New Zealand
| | - Anna J MacDonald
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium.,Aquatic Ecology, Evolution and Conservation, KULeuven, Charles Deberiotstraat 32, box 2439, 3000, Leuven, Belgium
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, 10700 104 Avenue, Edmonton, AB, T5J 4S2, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, Florida, 33701, USA
| | - David O'Brien
- NatureScot, Great Glen House, Leachkin Road, Inverness, IV3 8NW, UK
| | - Ivan Paz-Vinas
- Laboratoire Evolution et Diversité Biologique, Université de Toulouse, CNRS, IRD, UPS, UMR-5174 EDB, 118 route de Narbonne, Toulouse, 31062, France
| | - Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, 3041 Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, Via E. Mach, 1, San Michele all'Adige, 38010, (TN), Italy
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| |
Collapse
|
8
|
Yao Z, Wang X, Wang K, Yu W, Deng P, Dong J, Li Y, Cui K, Liu Y. Chloroplast and Nuclear Genetic Diversity Explain the Limited Distribution of Endangered and Endemic Thuja sutchuenensis in China. Front Genet 2021; 12:801229. [PMID: 35003229 PMCID: PMC8733598 DOI: 10.3389/fgene.2021.801229] [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: 10/25/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Narrow-ranged species face challenges from natural disasters and human activities, and to address why species distributes only in a limited region is of great significance. Here we investigated the genetic diversity, gene flow, and genetic differentiation in six wild and three cultivated populations of Thuja sutchuenensis, a species that survive only in the Daba mountain chain, using chloroplast simple sequence repeats (cpSSR) and nuclear restriction site-associated DNA sequencing (nRAD-seq). Wild T. sutchuenensis populations were from a common ancestral population at 203 ka, indicating they reached the Daba mountain chain before the start of population contraction at the Last Interglacial (LIG, ∼120-140 ka). T. sutchuenensis populations showed relatively high chloroplast but low nuclear genetic diversity. The genetic differentiation of nRAD-seq in any pairwise comparisons were low, while the cpSSR genetic differentiation values varied with pairwise comparisons of populations. High gene flow and low genetic differentiation resulted in a weak isolation-by-distance effect. The genetic diversity and differentiation of T. sutchuenensis explained its survival in the Daba mountain chain, while its narrow ecological niche from the relatively isolated and unique environment in the "refugia" limited its distribution.
Collapse
Affiliation(s)
- Zhi Yao
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Xinyu Wang
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kailai Wang
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Wenhao Yu
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Purong Deng
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jinyi Dong
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, China
| | - Yonghua Li
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kaifeng Cui
- Changbai Mountain Academy of Sciences, Joint Key Laboratory of Community and Biodiversity for Jilin Province and Changbai Mountain, Jilin, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| |
Collapse
|
9
|
Aavik T, Träger S, Zobel M, Honnay O, Van Geel M, Bueno CG, Koorem K. The joint effect of host plant genetic diversity and arbuscular mycorrhizal fungal communities on restoration success. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsipe Aavik
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Sabrina Träger
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
- Institute of Biology/Geobotany and Botanical Garden Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Martin Zobel
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Olivier Honnay
- Plant Conservation and Population Biology Biology Department University of Leuven Heverlee Belgium
| | - Maarten Van Geel
- Plant Conservation and Population Biology Biology Department University of Leuven Heverlee Belgium
| | - C. Guillermo Bueno
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Kadri Koorem
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| |
Collapse
|
10
|
Sheaves M, Waltham NJ, Benham C, Bradley M, Mattone C, Diedrich A, Sheaves J, Sheaves A, Hernandez S, Dale P, Banhalmi-Zakar Z, Newlands M. Restoration of marine ecosystems: Understanding possible futures for optimal outcomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148845. [PMID: 34274664 DOI: 10.1016/j.scitotenv.2021.148845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 05/17/2023]
Abstract
Accelerating declines in the extent, quality and functioning of the world's marine ecosystems have generated an upsurge in focus on practical solutions, with ecosystem restoration becoming an increasingly attractive mitigation strategy for systems as diverse as coral reefs, mangroves and tidal flats. While restoration is popular because it promises positive outcomes and a return to something approaching unimpacted condition and functioning, it involves substantial public and private investment, both for the initial restoration activity and for on-going maintenance of the restored asset. This investment often affords one big chance to get things right before irretrievable damage is done. As a result, precise, well considered and accountable decision-making is needed to determine the specific focus for restoration, the scale of restoration, the location for deploying restoration activities, and indeed whether or not restoration is necessary or even possible. We explore the environmental/ecological considerations and constraints governing optimal decisions about the nature, location and prioritisation of restoration activities in marine ecosystems, and in particular the constraints on achieving understanding of possible futures and the likelihood of achieving them. We conclude that action must be informed by a context-specific understanding of the historical situation, the current situation, the constraints on change, the range of potential outcome scenarios, and the potential futures envisioned.
Collapse
Affiliation(s)
- M Sheaves
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia.
| | - N J Waltham
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia; Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - C Benham
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, Queensland 4067, Australia
| | - M Bradley
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - C Mattone
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - A Diedrich
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - J Sheaves
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - A Sheaves
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - S Hernandez
- Marine Data Technology Hub, College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - P Dale
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland 4011, Australia
| | - Z Banhalmi-Zakar
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering, James Cook University, Queensland 4811, Australia
| | - M Newlands
- College of Arts, Society and Education, James Cook University, Queensland 4811, Australia
| |
Collapse
|
11
|
Höfner J, Klein‐Raufhake T, Lampei C, Mudrak O, Bucharova A, Durka W. Populations restored using regional seed are genetically diverse and similar to natural populations in the region. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Johannes Höfner
- Institute of Landscape Ecology University of Münster Münster Germany
- Department of Community Ecology (BZF) Helmholtz Centre for Environmental Research‐UFZ Halle Germany
| | | | - Christian Lampei
- Institute of Landscape Ecology University of Münster Münster Germany
| | - Ondrej Mudrak
- Institute of Botany of the Czech Academy of Sciences Třeboň Czech Republic
| | - Anna Bucharova
- Institute of Landscape Ecology University of Münster Münster Germany
- Department of Biology Philipps‐University Marburg Marburg Germany
| | - Walter Durka
- Department of Community Ecology (BZF) Helmholtz Centre for Environmental Research‐UFZ Halle Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| |
Collapse
|
12
|
Abstract
The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.
Collapse
|
13
|
McDonald G, Appleby MW, Sime H, Radford J, Hoffmann AA. Establishing a climate‐ready revegetation trial in central Victoria – A case study. ECOLOGICAL MANAGEMENT & RESTORATION 2021. [DOI: 10.1111/emr.12497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
14
|
Hoffmann AA, Miller AD, Weeks AR. Genetic mixing for population management: From genetic rescue to provenancing. Evol Appl 2021; 14:634-652. [PMID: 33767740 PMCID: PMC7980264 DOI: 10.1111/eva.13154] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.
Collapse
Affiliation(s)
- Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityWarrnamboolVic.Australia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | - Andrew R. Weeks
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
- cesar Pty LtdParkvilleVic.Australia
| |
Collapse
|
15
|
Jia Y, Milne RI, Zhu J, Gao L, Zhu G, Zhao G, Liu J, Li Z. Evolutionary legacy of a forest plantation tree species ( Pinus armandii): Implications for widespread afforestation. Evol Appl 2020; 13:2646-2662. [PMID: 33294014 PMCID: PMC7691453 DOI: 10.1111/eva.13064] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/21/2020] [Accepted: 07/01/2020] [Indexed: 11/29/2022] Open
Abstract
Many natural systems are subject to profound and persistent anthropogenic influence. Human-induced gene movement through afforestation and the selective transportation of genotypes might enhance the potential for intraspecific hybridization, which could lead to outbreeding depression. However, the evolutionary legacy of afforestation on the spatial genetic structure of forest tree species has barely been investigated. To do this properly, the effects of anthropogenic and natural processes must be examined simultaneously. A multidisciplinary approach, integrating phylogeography, population genetics, species distribution modeling, and niche divergence would permit evaluation of potential anthropogenic impacts, such as mass planting near-native material. Here, these approaches were applied to Pinus armandii, a Chinese endemic coniferous tree species, that has been mass planted across its native range. Population genetic analyses showed that natural populations of P. armandii comprised three lineages that diverged around the late Miocene, during a period of massive uplifts of the Hengduan Mountains, and intensification of Asian Summer Monsoon. Only limited gene flow was detected between lineages, indicating that each largely maintained is genetic integrity. Moreover, most or all planted populations were found to have been sourced within the same region, minimizing disruption of large-scale spatial genetic structure within P. armandii. This might be because each of the three lineages had a distinct climatic niche, according to ecological niche modeling and niche divergence tests. The current study provides empirical genetic and ecological evidence for the site-species matching principle in forestry and will be useful to manage restoration efforts by identifying suitable areas and climates for introducing and planting new forests. Our results also highlight the urgent need to evaluate the genetic impacts of large-scale afforestation in other native tree species.
Collapse
Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi’anChina
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Richard I. Milne
- Institute of Molecular Plant SciencesSchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Juan Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi’anChina
| | - Lian‐Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Guang‐Fu Zhu
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Gui‐Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi’anChina
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Zhong‐Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi’anChina
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| |
Collapse
|