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Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024; 24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Annie S Guillaume
- Geospatial Molecular Epidemiology group (GEOME), Laboratory for Biological Geochemistry (LGB), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arianna Kuhn
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- Virginia Museum of Natural History, Martinsville, Virginia, USA
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, Western Australia, Australia
| | - Ted Cosart
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Leif Howard
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Shawn R Narum
- Hagerman Genetics Lab, University of Idaho, Hagerman, Idaho, USA
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Helen R Taylor
- Royal Zoological Society of Scotland, Edinburgh, Scotland
| | - Gregg W C Thomas
- Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Maren Wellenreuther
- Plant and Food Research, Nelson, New Zealand
- University of Auckland, Auckland, New Zealand
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
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2
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Cullingham C, Peery RM, Miller JM. A roadmap to robust discriminant analysis of principal components. Mol Ecol Resour 2023; 23:519-522. [PMID: 36282622 DOI: 10.1111/1755-0998.13724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 10/31/2022]
Abstract
Identification of population structure is a common goal for a variety of applications, including conservation, wildlife management, and medical genetics. The outcome of these analyses can have far reaching implications; therefore, it is important to ensure an understanding of the strengths and weaknesses of the methodologies used. Increasing in popularity, the discriminant analysis of principal components (DAPC) method incorporates combinations of genetic variables (alleles) into a model that differentiates individuals into genetic clusters. However, users may not have a full understanding of how to best parameterize the model. In this issue of Thia (Molecular Ecology Resources, 2022) looks under the hood of the DAPC. Using simulated data, he demonstrates the importance of careful parameter selection in developing a DAPC model, what the implications are for over-fitting the model, and finally, how best to evaluate the results of DAPC models. This work highlights the issues that can arise when over-parameterizing the DAPC model when gene flow is high among clusters and provides important guidelines to ensure researchers are making conclusions that are biologically relevant.
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Affiliation(s)
| | - Rhiannon M Peery
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Joshua M Miller
- Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
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3
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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4
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Reid JM, Bignal E, Bignal S, McCracken DI, Fenn SR, Trask AE, Monaghan P. Integrating advances in population and evolutionary ecology with conservation strategy through long-term studies of red-billed choughs. J Anim Ecol 2021; 91:20-34. [PMID: 34679183 DOI: 10.1111/1365-2656.13615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022]
Abstract
Conceptual and methodological advances in population and evolutionary ecology are often pursued with the ambition that they will help identify demographic, ecological and genetic constraints on population growth rate (λ), and ultimately facilitate evidence-based conservation. However, such advances are often decoupled from conservation practice, impeding translation of scientific understanding into effective conservation and of conservation-motivated research into wider conceptual understanding. We summarise key outcomes from long-term studies of a red-billed chough Pyrrhocorax pyrrhocorax population of conservation concern, where we proactively aimed to achieve the dual and interacting objectives of advancing population and evolutionary ecology and advancing effective conservation. Estimation of means, variances and covariances in key vital rates from individual-based demographic data identified temporal and spatial variation in subadult survival as key constraints on λ, and simultaneously provided new insights into how vital rates can vary as functions of demographic structure, natal conditions and parental life history. Targeted analyses showed that first-year survival increased with prey abundance, implying that food limitation may constrain λ. First-year survival then decreased dramatically, threatening population viability and prompting emergency supplementary feeding interventions. Detailed evaluations suggested that the interventions successfully increased first-year survival in some years and additionally increased adult survival and successful reproduction, thereby feeding back to inform intervention refinements and understanding of complex ecological constraints on λ. Genetic analyses revealed novel evidence of expression of a lethal recessive allele, and demonstrated how critically small effective population size can arise, thereby increasing inbreeding and loss of genetic variation. Population viability analyses parameterised with all available demographic and genetic data showed how ecological and genetic constraints can interact to limit population viability, and identified ecological management as of primacy over genetic management to ensure short-term persistence of the focal population. This case study demonstrates a full iteration through the sequence of primary science, evidence-based intervention, quantitative evaluation and feedback that is advocated in conservation science but still infrequently achieved. It thereby illustrates how pure science advances informed conservation actions to ensure the (short-term) stability of the target population, and how conservation-motivated analyses fed back to advance fundamental understanding of population processes.
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Affiliation(s)
- Jane M Reid
- School of Biological Sciences, Zoology Building, University of Aberdeen, Aberdeen, UK.,Centre for Biodiversity Dynamics, Institutt for Biologi, NTNU, Trondheim, Norway
| | - Eric Bignal
- Scottish Chough Study Group, Kindrochaid, Bridgend, Isle of Islay, Argyll, UK
| | - Sue Bignal
- Scottish Chough Study Group, Kindrochaid, Bridgend, Isle of Islay, Argyll, UK
| | - Davy I McCracken
- Department of Integrated Land Management, Scotland's Rural College, Ayr, UK
| | - Sarah R Fenn
- School of Biological Sciences, Zoology Building, University of Aberdeen, Aberdeen, UK
| | - Amanda E Trask
- Institute of Zoology, Zoological Society of London, London, UK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health & Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK
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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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Gousy-Leblanc M, Yannic G, Therrien JF, Lecomte N. Mapping our knowledge on birds of prey population genetics. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Han EK, Cho WB, Park JS, Choi IS, Kwak M, Kim BY, Lee JH. A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak ( Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization. Genes (Basel) 2020; 11:E1114. [PMID: 32977695 PMCID: PMC7598624 DOI: 10.3390/genes11101114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.
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Affiliation(s)
- Eun-Kyeong Han
- Department of Biological Sciences and Biotechnology, Chonnam National University, Gwangju 61186, Korea;
| | - Won-Bum Cho
- Department of Biology Education, Chonnam National University, Gwangju 61186, Korea;
| | - Jong-Soo Park
- Department of Biological Sciences, Inha University, 100, Inha-ro, Michuhol-gu, Incheon 22212, Korea;
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Myounghai Kwak
- Biological and Genetic Resources Utilization Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Korea;
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Taft HR, McCoskey DN, Miller JM, Pearson SK, Coleman MA, Fletcher NK, Mittan CS, Meek MH, Barbosa S. Research–management partnerships: An opportunity to integrate genetics in conservation actions. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.218] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
| | | | - Joshua M. Miller
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
| | - Sarah K. Pearson
- College of Science and EngineeringFlinders University of South Australia Adelaide South Australia Australia
| | - Melinda A. Coleman
- Department of Primary Industries NSW FisheriesNational Marine Science Centre Coffs Harbour New South Wales Australia
- National Marine Science CentreSouthern Cross University Coffs Harbour New South Wales Australia
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary BiologyCornell University, Corson Hall Ithaca New York USA
| | - Cinnamon S. Mittan
- Department of Ecology and Evolutionary BiologyCornell University, Corson Hall Ithaca New York USA
| | - Mariah H. Meek
- Department of Integrative BiologyMichigan State University East Lansing Michigan USA
| | - Soraia Barbosa
- Department of Fish and Wildlife SciencesUniversity of Idaho Moscow Idaho USA
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9
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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10
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Species-specific genetic variation in response to deep-sea environmental variation amongst Vulnerable Marine Ecosystem indicator taxa. Sci Rep 2020; 10:2844. [PMID: 32071333 PMCID: PMC7028729 DOI: 10.1038/s41598-020-59210-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/27/2020] [Indexed: 11/15/2022] Open
Abstract
Understanding the ecological processes that shape spatial genetic patterns of population structure is critical for understanding evolutionary dynamics and defining significant evolutionary and management units in the deep sea. Here, the role of environmental factors (topographic, physico-chemical and biological) in shaping the population genetic structure of four deep-sea habitat-forming species (one sponge - Poecillastra laminaris, three corals - Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) was investigated using seascape genetics. Genetic data (nuclear and mitochondrial sequences and microsatellite multilocus genotypes) and environmental variables were employed to build individual-based and population-level models. The results indicated that environmental factors affected genetic variation differently amongst the species, as well as at different geographic scales. For individual-based analyses, different environmental variables explained genetic variation in P. laminaris (dissolved oxygen), G. dumosa (dynamic topography), M. oculata (sea surface temperature and surface water primary productivity), and S. variabilis (tidal current speed). At the population level, factors related to current and food source explained the regional genetic structure in all four species, whilst at the geomorphic features level, factors related to food source and topography were most important. Environmental variation in these parameters may be acting as barriers to gene flow at different scales. This study highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms, and to identify environmental factors that can be used to locate sites for the protection of deep-sea Vulnerable Marine Ecosystems.
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Abstract
Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 104-106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA;
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195-5020, USA;
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program and Biotechnology Institute, University of Helsinki, 00014 Helsinki, Finland;
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Vera-Escalona I, Habit E, Ruzzante DE. Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish. Proc Biol Sci 2019; 286:20182567. [PMID: 30963839 PMCID: PMC6408905 DOI: 10.1098/rspb.2018.2567] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/01/2019] [Indexed: 01/18/2023] Open
Abstract
The present distribution of Patagonian species is the result of a complex history involving Quaternary refugial populations, Holocene range expansions and demographic changes occurring during the Anthropocene. Invasive salmonids were introduced in Patagonia during the last century, occupying most rivers and lakes, preying on and competing with native species, including the fish Galaxias platei. Here, we used G. platei as a case study to understand how long-term (i.e. population differentiation during the Holocene) and short-term historical processes (salmonid introductions) affect genetic diversity. Using a suite of microsatellite markers, we found that the number of alleles is negatively correlated with the presence of salmonids (short-term processes), with G. platei populations from lakes with salmonids exhibiting significantly lower genetic diversity than populations from lakes without salmonids. Simulations (100 years backwards) showed that this difference in genetic diversity can be explained by a 99% reduction in population size. Allelic richness and observed heterozygosities were also negatively correlated with the presence of salmonids, but also positively correlated with long-term processes linked to Quaternary glaciations. Our results show how different genetic parameters can help identify processes taking place at different scales and their importance in terms of conservation.
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Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4R2
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Alonso de Ribera 2850, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n. Concepción, Casilla 160-C, Chile
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4R2
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Hegde S, Pai SR, Bhagwat RM, Saini A, Rathore PK, Jalalpure SS, Hegde HV, Sugunan AP, Gupta VS, Kholkute SD, Roy S. Genetic and phytochemical investigations for understanding population variability of the medicinally important tree Saraca asoca to help develop conservation strategies. PHYTOCHEMISTRY 2018; 156:43-54. [PMID: 30189346 DOI: 10.1016/j.phytochem.2018.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 08/02/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Saraca asoca (Roxb.) De Wilde (Caesalpiniaceae) is a highly traded IUCN red listed tree species used in Ayurvedic medicines for the treatment of various disorders, especially gynaecological problems. However, information about the genetic variations between populations and corresponding variation in specialized metabolites of S. asoca remains unclear. To address this issue, we analysed 11 populations of S. asoca with 106 accessions collected from Western Ghats of India using ISSR markers along with selected phytocompounds using RP-HPLC. Twenty primers were screened, out of which seven were selected for further analysis based on generation of clear polymorphic banding patterns. These seven ISSR primers produced 74 polymorphic loci. AMOVA showed 43% genetic variation within populations and 57% among the populations of S. asoca. To estimate the genetic relationships among S. asoca populations, UPGMA and Bayesian Models were constructed, which revealed two clusters of similar grouping patterns. However, excluding minor deviations, UPGMA and dissimilarity analysis showed close association of genotypes according to their geographical locations. Catechin (CAT), epicatechin (EPI) and gallic acid (GA) were quantified from bark and leaf samples of corresponding genotypes collected from 106 accessions. ROC plots depicted the sensitivity and specificity of the concentrations of tested phytocompounds at various cut-off points. Although, multiple logistic regression analysis predicted some association between few loci with GA, EPI and CAT, but PCA for phytochemical data failed to distinguish the populations. Overall, there were no significant trends observed to distinguish the populations based on these phytocompounds. Furthermore, the study advocates the delineate provenance regions of S. asoca genotypes/chemotype snapshots for in-situ conservation and ex-situ cultivation.
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Affiliation(s)
- Satisha Hegde
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India; KLE Academy of Higher Education and Research (Deemed-to-be-University), Dr. Prabhakar Kore Basic Science Research Center, Belagavi, Karnataka, 590010, India
| | - Sandeep Ramchandra Pai
- Amity Institute of Biotechnology, Amity University, Mumbai - Pune Expressway, Bhatan, Post - Somathne, Panvel, Mumbai, Maharashtra, 410206, India
| | - Rasika M Bhagwat
- Plant Molecular Biology Group, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Archana Saini
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Poonam Kanwar Rathore
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Sunil Satyappa Jalalpure
- KLE Academy of Higher Education and Research (Deemed-to-be-University), Dr. Prabhakar Kore Basic Science Research Center, Belagavi, Karnataka, 590010, India; Department of Pharmacognosy and Phytochemistry, College of Pharmacy, KLE Academy of Higher Education and Research (Deemed-to-be-University), Belagavi, Karnataka, 590010, India
| | - Harsha Vasudev Hegde
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Attayoor Purushottaman Sugunan
- Division of Epidemiology, RMRC-NIE-LRU, National Institute of Epidemiology, Indian Council of Medical Research, Department of Health Research, Government of India, Chennai, Tamil Nadu, 600 077, India
| | - Vidya S Gupta
- Plant Molecular Biology Group, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Sanjiva D Kholkute
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India
| | - Subarna Roy
- ICMR - National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research, Government of India, Belagavi, Karnataka, 590010, India.
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Underwood JN, Richards ZT, Miller KJ, Puotinen ML, Gilmour JP. Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral. Mol Ecol 2018; 27:1586-1602. [DOI: 10.1111/mec.14559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/22/2018] [Accepted: 02/24/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Jim N. Underwood
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Perth WA Australia
| | - Karen J. Miller
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Marji L. Puotinen
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - James P. Gilmour
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
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15
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16
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Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
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Torres-Florez JP, Johnson WE, Nery MF, Eizirik E, Oliveira-Miranda MA, Galetti PM. The coming of age of conservation genetics in Latin America: what has been achieved and what needs to be done. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1006-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Smith CT, Adams B, Bartron M, Burnham-Curtis MK, Monroe E, Olsen JB, Wilson WD, Williams A, Millard MJ, Webb MAH, Wenburg JK. Comment on Haig et al. (): the conservation genetics juggling act: integrating genetics and ecology, science and policy. Evol Appl 2017; 9:635-637. [PMID: 28435441 PMCID: PMC4869405 DOI: 10.1111/eva.12374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/24/2016] [Indexed: 12/03/2022] Open
Affiliation(s)
- Christian T Smith
- Abernathy Fish Technology Center U.S. Fish and Wildlife Service Longview WA USA
| | - Brice Adams
- Abernathy Fish Technology Center U.S. Fish and Wildlife Service Longview WA USA
| | - Meredith Bartron
- Northeast Fishery Center U.S. Fish and Wildlife Service Lamar PA USA
| | - Mary K Burnham-Curtis
- Clark R. Bavin National Fish and Wildlife Forensic Laboratory U.S. Fish and Wildlife Service Ashland OR USA
| | - Emy Monroe
- Whitney Genetics Laboratory U.S. Fish and Wildlife Service Onalaska WI USA
| | - Jeffrey B Olsen
- Conservation Genetics Laboratory U.S. Fish and Wildlife Service Anchorage AK USA
| | - Wade D Wilson
- Southwestern Native Aquatic Resources and Recovery Center U.S. Fish and Wildlife Service Dexter NM USA
| | - Ashantye' Williams
- Conservation Genetics Laboratory U.S. Fish and Wildlife Service Warm Springs GA USA
| | - Michael J Millard
- Northeast Fishery Center U.S. Fish and Wildlife Service Lamar PA USA
| | - Molly A H Webb
- Bozeman Fish Technology Center U.S. Fish and Wildlife Service Bozeman MT USA
| | - John K Wenburg
- Conservation Genetics Laboratory U.S. Fish and Wildlife Service Anchorage AK USA
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19
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R. Taylor H, Dussex N, van Heezik Y. Bridging the conservation genetics gap by identifying barriers to implementation for conservation practitioners. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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20
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A Bigger Toolbox: Biotechnology in Biodiversity Conservation. Trends Biotechnol 2017; 35:55-65. [DOI: 10.1016/j.tibtech.2016.06.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 01/08/2023]
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21
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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Haig SM. Response to Smith et al. 18 February 2016. Evol Appl 2016; 9:638-639. [PMID: 28435442 PMCID: PMC4869406 DOI: 10.1111/eva.12381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/17/2016] [Indexed: 11/29/2022] Open
Affiliation(s)
- Susan M. Haig
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis OR USA
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23
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Wellenreuther M, Otto S. Women in evolution - highlighting the changing face of evolutionary biology. Evol Appl 2016; 9:3-16. [PMID: 27087836 PMCID: PMC4780375 DOI: 10.1111/eva.12343] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/20/2015] [Indexed: 12/16/2022] Open
Abstract
The face of science has changed. Women now feature alongside men at the forefront of many fields, and this is particularly true in evolutionary biology. This special issue celebrates the outstanding achievements and contributions of women in evolutionary biology, by highlighting a sample of their research and accomplishments. In addition to original research contributions, this collection of articles contains personal reflections to provide perspective and advice on succeeding as a woman in science. By showcasing the diversity and research excellence of women and drawing on their experiences, we wish to enhance the visibility of female scientists and provide inspiration as well as role models. These are exciting times for evolutionary biology, and the field is richer and stronger for the diversity of voices contributing to the field.
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Affiliation(s)
- Maren Wellenreuther
- Department of BiologyUniversity of LundLundSweden
- Institute for Plant and Food ResearchLundNew Zealand
| | - Sarah Otto
- Department of Zoology & Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
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