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Kristensen TN, Schönherz AA, Rohde PD, Sørensen JG, Loeschcke V. Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles. Sci Rep 2024; 14:17789. [PMID: 39090347 PMCID: PMC11294339 DOI: 10.1038/s41598-024-68753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
There is experimental evidence that microbiomes have a strong influence on a range of host traits. Understanding the basis and importance of symbiosis between host and associated microorganisms is a rapidly developing research field, and we still lack a mechanistic understanding of ecological and genetic pressures affecting host-microbiome associations. Here Drosophila melanogaster lines from a large-scale artificial selection experiment were used to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions for two generations prior to assessment. Our findings provide strong evidence for symbiosis between host and microbiomes but we cannot reveal whether the interactions are adaptive, nor whether they are caused by genetic or ecological factors.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - Anna A Schönherz
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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2
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Wang X, Reid K, Chen Y, Dudgeon D, Merilä J. Ecological genetics of isolated loach populations indicate compromised adaptive potential. Heredity (Edinb) 2024; 133:88-98. [PMID: 38961235 PMCID: PMC11286901 DOI: 10.1038/s41437-024-00695-0] [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: 01/10/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.
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Affiliation(s)
- Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Chen
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - David Dudgeon
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, FI-00014 University of Helsinki, Helsinki, Finland.
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3
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Onorato DP, Cunningham MW, Lotz M, Criffield M, Shindle D, Johnson A, Clemons BCF, Shea CP, Roelke-Parker ME, Johnson WE, McClintock BT, Pilgrim KL, Schwartz MK, Oli MK. Multi-generational benefits of genetic rescue. Sci Rep 2024; 14:17519. [PMID: 39080286 PMCID: PMC11289468 DOI: 10.1038/s41598-024-67033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Genetic rescue-an increase in population fitness following the introduction of new alleles-has been proven to ameliorate inbreeding depression in small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue in wildlife conservation is how long beneficial effects persist in admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers (Puma concolor coryi) across nine generations, we show that the experimental genetic rescue implemented in 1995-via the release of eight female pumas from Texas-alleviated morphological, genetic, and demographic correlates of inbreeding depression, subsequently preventing extirpation of the population. We present unequivocal evidence, for the first time in any terrestrial vertebrate, that genetic and phenotypic benefits of genetic rescue remain in this population after five generations of admixture, which helped increase panther abundance (> fivefold) and genetic effective population size (> 20-fold). Additionally, even with extensive admixture, microsatellite allele frequencies in the population continue to support the distinctness of Florida panthers from other North American puma populations, including Texas. Although threats including habitat loss, human-wildlife conflict, and infectious diseases are challenges to many imperiled populations, our results suggest genetic rescue can serve as an effective, multi-generational tool for conservation of small, isolated populations facing extinction from inbreeding.
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Affiliation(s)
- Dave P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Rd, Naples, FL, 34114, USA.
| | - Mark W Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Mark Lotz
- Division of Habitat and Species Conservation, Florida Fish and Wildlife Conservation Commission, Naples, FL, 34114, USA
| | - Marc Criffield
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Rd, Naples, FL, 34114, USA
| | - David Shindle
- US Fish and Wildlife Service, Florida Ecological Services Field Office, Immokalee, FL, 34142, USA
| | - Annette Johnson
- Big Cypress National Preserve, National Park Service, Ochopee, FL, 34141, USA
| | - Bambi C F Clemons
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Colin P Shea
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA
| | | | - Warren E Johnson
- Department of Biology, Loyola University of Maryland, Baltimore, MD, 21210, USA
| | - Brett T McClintock
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Seattle, WA, 98115, USA
| | - Kristine L Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, 59801, USA
| | - Michael K Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, 59801, USA
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA
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4
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Napolitano C, Clavijo C, Rojas-Bonzi V, Miño CI, González-Maya JF, Bou N, Giraldo A, Martino A, Miyaki CY, Aguirre LF, Cosacov A, Milián-García Y, Prosdocimi L, Ramírez-Bravo OE, Tovar LA, Velez-Zuazo X, Barrios M, Herrera-Fernández B, Montiel-Villalobos MG, Oliveira-Miranda MA, Pool M, Santos-Murgas A, Segovia-Salcedo MC, Cecchi F, Dans AJ, Dilchand N, Lima SMQ, Novas MC, Pelz-Serrano K, Pougy N, Rodríguez I, van der Meer L, Zapata-Ríos G. Understanding the conservation-genetics gap in Latin America: challenges and opportunities to integrate genetics into conservation practices. Front Genet 2024; 15:1425531. [PMID: 39040996 PMCID: PMC11261212 DOI: 10.3389/fgene.2024.1425531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/04/2024] [Indexed: 07/24/2024] Open
Abstract
Introduction: Integrating genetic data into conservation management decisions is a challenging task that requires strong partnerships between researchers and managers. Conservation in Latin America is of crucial relevance worldwide given the high biodiversity levels and the presence of hotspots in this region. Methods: We conducted a survey across Latin America to identify gaps and opportunities between genetic researchers and conservation managers. We aimed to better understand conservation managers' points of view and how genetic research could help conservation practitioners to achieve their goals, by implementing genetic assessments that could effectively inform conservation practices. We distributed an online survey via four regional collaborating organizations and 32 focal points based in 20 Latin American countries. The target respondents were conservation managers of species or areas in Latin America. Results: We collected a total of 468 answered questionnaires from 21 Latin American countries. Most respondents (44%) were from an academic or research institution while non-academics were mainly from non-governmental institutions (30%) and government agencies (25%). Most respondents (65%) have performed or used genetic assessments in their managed area or species, either alone, in partnership, contracting someone else or using published results. For the majority of this group, the genetic results were relevant to their conservation management goals, helping to inform management decisions. Respondents that had not performed genetic assessments (35%) were mainly from the non-academic group, and their main barriers were limited access to funds, genetic lab facilities, and trained personnel to design studies and conduct lab work. Discussion: From the findings, we describe the current situation and provide a general diagnosis of the conservation-genetics gap in Latin America. We describe the gender gap, academic-practitioner co-development of conservation questions and projects, and the nationality and residency of Latin American conservation managers in relation to the countries where they work. We discuss opportunities to co-create research questions and co-develop studies based on conservation practitioners' needs. We offer recommendations for overcoming barriers to integrate genetic information into conservation actions, and advance agendas that fit the needs and realities of the highly heterogeneous, biodiverse and challenging Latin American region.
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Affiliation(s)
- Constanza Napolitano
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
| | | | - Viviana Rojas-Bonzi
- Instituto de Investigación Biológica del Paraguay, Asuncion, Paraguay
- Wildlife Ecology and Conservation Department, University of Florida, Gainesville, FL, United States
| | - Carolina I. Miño
- Laboratorio de Genética Evolutiva - LGE, Instituto de Biología Subtropical - IBS, Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET, Universidad Nacional de Misiones (UNaM), Posadas, Argentina
| | - José F. González-Maya
- Área de Biología de la Conservación, Departamento de Ciencias Ambientales, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Bogotá, Colombia
| | - Nadia Bou
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alan Giraldo
- Grupo de Investigación en Ecología Animal, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali, Colombia
| | - Angela Martino
- Centro de Investigaciones en Ecología y Zonas Aridas, Universidad Nacional Experimental Francisco de Miranda, Coro, Venezuela
| | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luis F. Aguirre
- Centro de Biodiversidad y Genética, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Andrea Cosacov
- Laboratorio de Ecología Evolutiva y Biología Floral, Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Laura Prosdocimi
- Laboratorio de Ecología, Comportamiento y Mamíferos Marinos (LECyMM), Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - O. Eric Ramírez-Bravo
- Centro de Agroecología, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Eco campus Valsequillo, San Pedro Zacachimalpa, Mexico
| | - Luis Antonio Tovar
- Facultad de Ciencias Forestales, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Ximena Velez-Zuazo
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC, United States
| | - Mercedes Barrios
- Centro de Datos para la Conservación, Centro de Estudios Conservacionistas, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
| | - Bernal Herrera-Fernández
- Instituto Internacional de Conservación y Manejo de Vida Silvestre (ICOMVIS), Universidad Nacional, Heredia, Costa Rica
| | | | | | - Monique Pool
- Green Heritage Fund Suriname, Paramaribo, Suriname
| | - Alonso Santos-Murgas
- Departamento de Zoología, Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá. Estación Científica Coiba AIP, Ciudad del Saber, Panama
| | | | - Felipe Cecchi
- Grupo Antropología de la Conservación, Universidad de Los Lagos, Osorno, Chile
| | - Armando J. Dans
- Departamento de Ciencias Ambientales y Producción Sostenible, Universidad de las Regiones Autónomas de la Costa Caribe Nicaragüense, Bluefields, Nicaragua
| | - Nelanie Dilchand
- Aquatic and Terrestrial Pioneers Consulting Services, Georgetown, Guyana
| | - Sergio M. Q. Lima
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - María Caridad Novas
- División de Conservación, Departamento de Botánica, Jardín Botánico Nacional Dr. Rafael María Moscoso, Santo Domingo, Dominican Republic
| | - Karla Pelz-Serrano
- Departamento de Ciencias Ambientales, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Lerma, Mexico
| | - Nina Pougy
- Departamento de Desenvolvimento Científico, Museu do Amanhã, Instituto de Desenvolvimento e Gestão - IDG, Rio de Janeiro, Brazil
| | - Iris Rodríguez
- Escuela de Biología, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
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5
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Wei S, Fan H, Zhou W, Huang G, Hua Y, Wu S, Wei X, Chen Y, Tan X, Wei F. Conservation genomics of the critically endangered Chinese pangolin. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2540-y. [PMID: 38970727 DOI: 10.1007/s11427-023-2540-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/07/2024] [Indexed: 07/08/2024]
Abstract
The Chinese pangolin (Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters (MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.
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Affiliation(s)
- Shichao Wei
- Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Huizhong Fan
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Guangping Huang
- Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Shibao Wu
- School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Xiao Wei
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, 530003, China
| | - Yiting Chen
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Xinyue Tan
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Fuwen Wei
- Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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6
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Aitken SN, Jordan R, Tumas HR. Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:707-736. [PMID: 38594931 DOI: 10.1146/annurev-arplant-070523-044239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.
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Affiliation(s)
- Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| | | | - Hayley R Tumas
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
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7
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Sexton JP, Clemens M, Bell N, Hall J, Fyfe V, Hoffmann AA. Patterns and effects of gene flow on adaptation across spatial scales: implications for management. J Evol Biol 2024; 37:732-745. [PMID: 38888218 DOI: 10.1093/jeb/voae064] [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: 09/16/2023] [Revised: 03/21/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.
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Affiliation(s)
- Jason P Sexton
- Department of Life and Environmental Sciences, University of California, Merced, CA, United States
| | - Molly Clemens
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Nicholas Bell
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Joseph Hall
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Verity Fyfe
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
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8
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Bonassin L, Pârvulescu L, Boštjančić LL, Francesconi C, Paetsch J, Rutz C, Lecompte O, Theissinger K. Genomic insights into the conservation status of the Idle Crayfish Austropotamobius bihariensis Pârvulescu, 2019: low genetic diversity in the endemic crayfish species of the Apuseni Mountains. BMC Ecol Evol 2024; 24:78. [PMID: 38862896 PMCID: PMC11165767 DOI: 10.1186/s12862-024-02268-5] [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: 10/30/2023] [Accepted: 06/05/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely. RESULTS Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins. CONCLUSION Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.
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Affiliation(s)
- Lena Bonassin
- Department of Computer Science, Centre de Recherche en Biomédecine de Strasbourg, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, ICube, Strasbourg, France
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, Department of Molecular Ecology, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829, Landau, Germany
| | - Lucian Pârvulescu
- Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Str. Pestalozzi 16A, 300115, Timisoara, Romania.
- Crayfish Research Centre, Institute for Advanced Environmental Research, West University of Timisoara, Oituz 4, 300086, Timisoara, Romania.
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, Centre de Recherche en Biomédecine de Strasbourg, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, ICube, Strasbourg, France
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, Department of Molecular Ecology, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829, Landau, Germany
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, Department of Molecular Ecology, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829, Landau, Germany
| | - Judith Paetsch
- Department of Biogeography, University of Trier, Behringstraße 21, D-54296, Geozentrum, Trier, Germany
| | - Christelle Rutz
- Department of Computer Science, Centre de Recherche en Biomédecine de Strasbourg, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, ICube, Strasbourg, France
| | - Odile Lecompte
- Department of Computer Science, Centre de Recherche en Biomédecine de Strasbourg, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, ICube, Strasbourg, France
| | - Kathrin Theissinger
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, D-35392, Giessen, Germany
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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.
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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
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10
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Sopniewski J, Catullo RA. Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong. Mol Ecol Resour 2024; 24:e13947. [PMID: 38433491 DOI: 10.1111/1755-0998.13947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.
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Affiliation(s)
- Jarrod Sopniewski
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Renee A Catullo
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
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11
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Cox-Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii). Mol Ecol 2024:e17362. [PMID: 38682494 DOI: 10.1111/mec.17362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Karah Cox-Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
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12
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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13
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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14
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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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15
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone ( Haliotis cracherodii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577275. [PMID: 38352393 PMCID: PMC10862700 DOI: 10.1101/2024.01.26.577275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Karah Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064 USA
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16
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Pegueroles C, Pascual M, Carreras C. Going beyond a reference genome in conservation genomics. Trends Ecol Evol 2024; 39:13-15. [PMID: 38040545 DOI: 10.1016/j.tree.2023.11.009] [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: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
The current biodiversity crisis demands scientifically based management. The generation of reference genomes is crucial in conservation, but is not enough to capture species diversity. By incorporating whole-genome sequencing (WGS) at the population level, Nigenda-Morales et al. provide key genomic information for the conservation of fin whale populations in the Pacific.
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Affiliation(s)
- Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Av. Diagonal 643. E08028, Barcelona, Spain.
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17
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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [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: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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18
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Xu H, Hu T, Li X, Song L, Yang S, Meng L, Turlings TCJ, Li B. Adaptive changes in pheromone production and release under rearing conditions in stink bugs. PEST MANAGEMENT SCIENCE 2023. [PMID: 38145909 DOI: 10.1002/ps.7950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Healthy cultures of arthropods are important for pest management programs (e.g. biocontrol). Little is known about how rearing conditions may affect pheromonal interactions. We investigated how rearing histories and densities affect pheromone emission/production in two stink bug species (Hemiptera: Heteroptera), the predatory bug Arma custos, a biocontrol agent, and the bean bug Riptortus pedestris, a pest on legume crops. RESULTS Nymphs from newly established laboratory colonies of both species produced higher amounts of the defense (dispersal) compound, 4-oxo-(E)-hexenal (OHE), in the presence of conspecific nymphs. Also, when two or more A. custos males were placed together, the dorsal abdominal glands (DAGs) ceased to release aggregation pheromone, whereas the metathoracic glands (MTGs) increased the emission of defensive odors. These changes resulted from exposure to conspecific pheromone odors, as confirmed by exposing bugs to pheromone standards. Hence, pheromone emissions in these stink bugs are readily changed in response to the odors of conspecifics, which may become a problem after long-term rearing. Indeed, an old laboratory colony of A. custos (~30 generations) exhibited less-developed DAGs and reduced pheromone production. Instead, males released significantly more defensive odors from the enlarged MTGs. Furthermore, long-term rearing conditions appeared to favor nymphs that were able to share space with conspecifics by releasing less OHE, which has not yet occurred in the new laboratory colonies. CONCLUSION Rearing density affects pheromone release in newly established laboratory colonies of stink bug species, whereas long-term rearing results in new pheromonal compositions coinciding with adaptive changes in gland development. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Hao Xu
- Key Laboratory of Soybean Disease and Pest Control, Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Tingxia Hu
- Key Laboratory of Soybean Disease and Pest Control, Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xingpeng Li
- Jilin Provincial Key Laboratory of Insect Biodiversity and Ecosystem Function of Changbai Mountains, Beihua University, Jilin, China
| | - Liwen Song
- Jilin Provincial Academy of Forestry Science, Changchun, China
| | - Shaohang Yang
- Key Laboratory of Soybean Disease and Pest Control, Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ling Meng
- Key Laboratory of Soybean Disease and Pest Control, Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ted C J Turlings
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Baoping Li
- Key Laboratory of Soybean Disease and Pest Control, Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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19
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Diaz‐Martin Z, De Vitis M, Havens K, Kramer AT, MacKechnie LM, Fant J. Species-specific effects of production practices on genetic diversity in plant reintroduction programs. Evol Appl 2023; 16:1956-1968. [PMID: 38143906 PMCID: PMC10739063 DOI: 10.1111/eva.13614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/26/2023] Open
Abstract
Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pretreatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three Viola species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pretreatments.
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Affiliation(s)
- Zoe Diaz‐Martin
- Department of BiologySpelman CollegeAtlantaGeorgiaUSA
- Chicago Botanic GardenNegaunee Institute for Plant Conservation Science and ActionGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
| | - Marcello De Vitis
- Chicago Botanic GardenNegaunee Institute for Plant Conservation Science and ActionGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
- Southeastern Grasslands InstituteAustin Peay State UniversityClarksvilleTennesseeUSA
| | - Kayri Havens
- Chicago Botanic GardenNegaunee Institute for Plant Conservation Science and ActionGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
| | - Andrea T. Kramer
- Chicago Botanic GardenNegaunee Institute for Plant Conservation Science and ActionGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
| | | | - Jeremie Fant
- Chicago Botanic GardenNegaunee Institute for Plant Conservation Science and ActionGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
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20
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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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21
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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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22
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Hu B, Han S, He H. Effect of epidemic diseases on wild animal conservation. Integr Zool 2023; 18:963-980. [PMID: 37202360 DOI: 10.1111/1749-4877.12720] [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] [Indexed: 05/20/2023]
Abstract
Under the background of global species extinction, the impact of epidemic diseases on wild animal protection is increasingly prominent. Here, we review and synthesize the literature on this topic, and discuss the relationship between diseases and biodiversity. Diseases usually reduce species diversity by decreasing or extinction of species populations, but also accelerate species evolution and promote species diversity. At the same time, species diversity can regulate disease outbreaks through dilution or amplification effects. The synergistic effect of human activities and global change is emphasized, which further aggravates the complex relationship between biodiversity and diseases. Finally, we emphasize the importance of active surveillance of wild animal diseases, which can protect wild animals from potential diseases, maintain population size and genetic variation, and reduce the damage of diseases to the balance of the whole ecosystem and human health. Therefore, we suggest that a background survey of wild animal populations and their pathogens should be carried out to assess the impact of potential outbreaks on the population or species level. The mechanism of dilution and amplification effect between species diversity and diseases of wild animals should be further studied to provide a theoretical basis and technical support for human intervention measures to change biodiversity. Most importantly, we should closely combine the protection of wild animals with the establishment of an active surveillance, prevention, and control system for wild animal epidemics, in an effort to achieve a win-win situation between wild animal protection and disease control.
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Affiliation(s)
- Bin Hu
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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23
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Chen S, Li W, Li W, Liu Z, Shi X, Zou Y, Liao W, Fan Q. Population genetics of Camellia granthamiana, an endangered plant species with extremely small populations in China. Front Genet 2023; 14:1252148. [PMID: 37867601 PMCID: PMC10585715 DOI: 10.3389/fgene.2023.1252148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction: Camellia, the largest genus of Theaceae, is well-known for having high economic values. Camellia granthamiana demonstrates large beautiful flowers with some primitive characters, such as multiple large and persistent bracteoles and sepals, was listed as Vulnerable species on the IUCN Red List. Methods: In this study, we investigated all possible records of the species, and sampled four natural populations and five cultivated individuals. By applying shallow-genome sequencing for nine individuals and RAD-seq sequencing for all the sampled 77 individuals, we investigated population genetic diversity and population structure of the species. Results and discussion: The results showed that the population sampled from Fengkai, previously identified as C. albogigias, possessed different plastid genome from other species possibly due to plastid capture; the species possesses strong population structure possibly due to the effect of isolation by distance, habitat fragmentation, and self-crossing tendency of the species, whose effective population size declined quickly in the past 4,000 years. Nevertheless, C. granthamiana maintains a medium level of genetic diversity within population, and significant differentiation was observed among the four investigated populations, it is anticipated that more populations are expected to be found and all these extant populations should be taken into instant protection.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenyan Li
- Shenzhen Dapeng Peninsula National Geopark, Shenzhen, China
| | - Wei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zhongcheng Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xianggang Shi
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yanli Zou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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24
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Tesfa D, Feyissa T, Assefa K. Genetic diversity and population structure of selected tef core germplasm lines based on microsatellite markers. Mol Biol Rep 2023; 50:8603-8613. [PMID: 37653359 DOI: 10.1007/s11033-023-08732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Tef is an indigenous and important food, feed, and cash crop for smallholder Ethiopian farmers. Knowledge of the natural genetic composition of the crop provides the option to further exploit its genetic potential through breeding. However, there are insufficient reports on the genetic variability of Ethiopian tef using a medium-throughput marker system. Hence, the current study was designed to evaluate the genetic variability of released and core germplasm that was collected earlier. METHODS AND RESULTS Eighty-one tef genotypes collected from eight Ethiopian ecological zones and released varieties were targeted using 14 SSR markers. The study yielded a total of 122 alleles across the entire locus and population. The molecular variance analysis indicated the existence of large genetic differentiation (FIS and FIT = 0.87), with 86% and 13% of the total variation accounted for among genotypes within the population and across all genotypes used for this study, respectively. However, low genetic differentiation among the populations (FST = 0.014, which accounts for 1%) was observed. Multivariate analyses such as clustering and PCoA did not cluster genotypes into distinct groups according to their geographical areas of population. This is presumably due to gene flow among populations. CONCLUSION In conclusion, our findings show that there is significant genetic diversity within populations, particularly in the Jimma, Tigray, and released varieties, as well as the presence of private alleles and heterozygosity. The study also indicates the existence of genotypic admixture in the studied materials. The identification of private alleles and their differentiation will be helpful in selecting breeding materials and creating breeding plans.
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Affiliation(s)
- Derejaw Tesfa
- Debereziet Agricultural Research Center, Ethiopian Institute of Agricultural Research, Bishoftu, Ethiopia.
- Institute of Biotechnology, Addis Abeba University, Addis Abeba, Ethiopia.
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Abeba University, Addis Abeba, Ethiopia
| | - Kebebew Assefa
- Debereziet Agricultural Research Center, Ethiopian Institute of Agricultural Research, Bishoftu, Ethiopia
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25
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Nistelberger HM, Roycroft E, Macdonald AJ, McArthur S, White LC, Grady PGS, Pierson J, Sims C, Cowen S, Moseby K, Tuft K, Moritz C, Eldridge MDB, Byrne M, Ottewell K. Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur. Mol Ecol 2023. [PMID: 37715549 DOI: 10.1111/mec.17119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.
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Affiliation(s)
- Heidi M Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Emily Roycroft
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna J Macdonald
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Lauren C White
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer Pierson
- Australian Wildlife Conservancy, Subiaco, Western Australia, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Moseby
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mark D B Eldridge
- Terrestrial Vertebrates, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
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26
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Watowich MM, Chiou KL, Graves B, tague MJM, Brent LJ, Higham JP, Horvath JE, Lu A, Martinez MI, Platt ML, Schneider-Crease IA, Lea AJ, Snyder-Mackler N. Best practices for genotype imputation from low-coverage sequencing data in natural populations. Mol Ecol Resour 2023:10.1111/1755-0998.13854. [PMID: 37602981 PMCID: PMC10879460 DOI: 10.1111/1755-0998.13854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/01/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023]
Abstract
Monitoring genetic diversity in wild populations is a central goal of ecological and evolutionary genetics and is critical for conservation biology. However, genetic studies of nonmodel organisms generally lack access to species-specific genotyping methods (e.g. array-based genotyping) and must instead use sequencing-based approaches. Although costs are decreasing, high-coverage whole-genome sequencing (WGS), which produces the highest confidence genotypes, remains expensive. More economical reduced representation sequencing approaches fail to capture much of the genome, which can hinder downstream inference. Low-coverage WGS combined with imputation using a high-confidence reference panel is a cost-effective alternative, but the accuracy of genotyping using low-coverage WGS and imputation in nonmodel populations is still largely uncharacterized. Here, we empirically tested the accuracy of low-coverage sequencing (0.1-10×) and imputation in two natural populations, one with a large (n = 741) reference panel, rhesus macaques (Macaca mulatta), and one with a smaller (n = 68) reference panel, gelada monkeys (Theropithecus gelada). Using samples sequenced to coverage as low as 0.5×, we could impute genotypes at >95% of the sites in the reference panel with high accuracy (median r2 ≥ 0.92). We show that low-coverage imputed genotypes can reliably calculate genetic relatedness and population structure. Based on these data, we also provide best practices and recommendations for researchers who wish to deploy this approach in other populations, with all code available on GitHub (https://github.com/mwatowich/LoCSI-for-non-model-species). Our results endorse accurate and effective genotype imputation from low-coverage sequencing, enabling the cost-effective generation of population-scale genetic datasets necessary for tackling many pressing challenges of wildlife conservation.
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Affiliation(s)
- Marina M. Watowich
- Department of Biology, University of Washington; Seattle, WA, 98195 USA
- Department of Biological Sciences, Vanderbilt University; Nashville, TN, 37235
| | - Kenneth L. Chiou
- Center for Evolution and Medicine, Arizona State University; Tempe, AZ, 85281 USA
- School of Life Sciences, Arizona State University; Tempe, AZ, 85281 USA
| | - Brian Graves
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign; Urbana, IL 61801
| | - Michael J. Mon tague
- Department of Neuroscience, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren J.N. Brent
- Centre for Research in Animal Behaviour, University of Exeter; Exeter EX4 4QG, UK
| | - James P. Higham
- Department of Anthropology, New York University; New York, NY 10003, USA
- New York Consortium in Evolutionary Primatology; New York, NY, 10016 USA
| | - Julie E. Horvath
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, NC 27707, USA
- Research and Collections Section, North Carolina Museum of Natural Sciences; Raleigh, NC 27601, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, NC 27708, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Melween I. Martinez
- Caribbean Primate Research Center, Unit of Comparative Medicine, University of Puerto Rico; San Juan, PR 00936, USA
| | - Michael L. Platt
- Department of Neuroscience, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
- Marketing Department, Wharton School of Business; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - India A. Schneider-Crease
- Center for Evolution and Medicine, Arizona State University; Tempe, AZ, 85281 USA
- School of Life Sciences, Arizona State University; Tempe, AZ, 85281 USA
- School of Human Evolution and Social Change, Arizona State University; Tempe, AZ, 85281 USA
| | - Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, 37235, USA
- Child and Brain Development, Canadian Institute for Advanced Research, Toronto, Canada
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University; Tempe, AZ, 85281 USA
- School of Life Sciences, Arizona State University; Tempe, AZ, 85281 USA
- School of Human Evolution and Social Change, Arizona State University; Tempe, AZ, 85281 USA
- Neurodegenerative Disease Research Center, Arizona State University; Tempe, AZ, 85281 USA
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27
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Tran DV, Vu TT, Fukutani K, Nishikawa K. Demographic and ecological niche dynamics of the Vietnam warty newt, Paramesotriton deloustali: Historical climate influences. PLoS One 2023; 18:e0290044. [PMID: 37594998 PMCID: PMC10437943 DOI: 10.1371/journal.pone.0290044] [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: 03/08/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023] Open
Abstract
Quaternary climatic cycles strongly affected the genetic diversification and ranges of organisms, shaping current genetic structures and distribution patterns. Urodeles provide ideal examples for exploring these dynamics over time and across space. In this study, we integrated a phylogeographic approach and ensemble species distribution modeling (eSDM) to infer the historical demography and distribution patterns of the Vietnam warty newt, Paramesotriton deloustali. Mitochondrial data revealed two groups, West and East, which diverged approximately 1.92 million years ago (Mya). Diversification was likely driven by change in the climate during early stages of the Pleistocene, with increasing monsoon and drought intensities. Biogeographic analysis indicated that the newt's current distribution formed as a result of vicariance events. In addition, the two groups occupy distinct ecological niches. Demographic reconstruction showed signs of expansion in the effective population sizes of the two major groups beginning around 0.11 and 0.15 Mya, respectively. However, eSDM showed fluctuating predicted distributions during the last interglacial, last glacial maximum, mid-Holocene, and present. Mountain systems in northern Vietnam are likely to have served as climatic refuges and to have played a crucial role in safeguarding species from the effects of climate change.
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Affiliation(s)
- Dung Van Tran
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Wildlife Department, Vietnam National University of Forestry, Ha Noi, Vietnam
| | - Thinh Tien Vu
- Wildlife Department, Vietnam National University of Forestry, Ha Noi, Vietnam
| | - Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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28
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Legge S, Rumpff L, Garnett ST, Woinarski JCZ. Loss of terrestrial biodiversity in Australia: Magnitude, causation, and response. Science 2023; 381:622-631. [PMID: 37561866 DOI: 10.1126/science.adg7870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/08/2023] [Indexed: 08/12/2023]
Abstract
Australia's biota is species rich, with high rates of endemism. This natural legacy has rapidly diminished since European colonization. The impacts of invasive species, habitat loss, altered fire regimes, and changed water flows are now compounded by climate change, particularly through extreme drought, heat, wildfire, and flooding. Extinction rates, already far exceeding the global average for mammals, are predicted to escalate across all taxa, and ecosystems are collapsing. These losses are symptomatic of shortcomings in resourcing, law, policy, and management. Informed by examples of advances in conservation practice from invasive species control, Indigenous land management, and citizen science, we describe interventions needed to enhance future resilience. Many characteristics of Australian biodiversity loss are globally relevant, with recovery requiring society to reframe its relationship with the environment.
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Affiliation(s)
- Sarah Legge
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, Northern Territory, Australia
- Fenner School of Society and the Environment, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Libby Rumpff
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen T Garnett
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - John C Z Woinarski
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, Northern Territory, Australia
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29
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Paxton KL, Cassin-Sackett L, Atkinson CT, Videvall E, Campana MG, Fleischer RC. Gene expression reveals immune response strategies of naïve Hawaiian honeycreepers experimentally infected with introduced avian malaria. J Hered 2023; 114:326-340. [PMID: 36869776 DOI: 10.1093/jhered/esad017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/01/2023] [Indexed: 03/05/2023] Open
Abstract
The unprecedented rise in the number of new and emerging infectious diseases in the last quarter century poses direct threats to human and wildlife health. The introduction to the Hawaiian archipelago of Plasmodium relictum and the mosquito vector that transmits the parasite has led to dramatic losses in endemic Hawaiian forest bird species. Understanding how mechanisms of disease immunity to avian malaria may evolve is critical as climate change facilitates increased disease transmission to high elevation habitats where malaria transmission has historically been low and the majority of the remaining extant Hawaiian forest bird species now reside. Here, we compare the transcriptomic profiles of highly susceptible Hawai'i 'amakihi (Chlorodrepanis virens) experimentally infected with P. relictum to those of uninfected control birds from a naïve high elevation population. We examined changes in gene expression profiles at different stages of infection to provide an in-depth characterization of the molecular pathways contributing to survival or mortality in these birds. We show that the timing and magnitude of the innate and adaptive immune response differed substantially between individuals that survived and those that succumbed to infection, and likely contributed to the observed variation in survival. These results lay the foundation for developing gene-based conservation strategies for Hawaiian honeycreepers by identifying candidate genes and cellular pathways involved in the pathogen response that correlate with a bird's ability to recover from malaria infection.
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Affiliation(s)
- Kristina L Paxton
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Hawai'i Cooperative Studies Unit, University of Hawai'i Hilo, PO Box 44, Hawai'i National Park, HI 96718, USA
| | - Loren Cassin-Sackett
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Department of Biology, University of Louisiana, Lafayette, LA 70503, USA
| | - Carter T Atkinson
- U.S. Geological Survey Pacific Island Ecosystems Research Center, PO Box 44, Hawai'i National Park, HI 96718, USA
| | - Elin Videvall
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Michael G Campana
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
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30
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Fitzpatrick SW, Mittan-Moreau C, Miller M, Judson JM. Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States. J Hered 2023; 114:354-366. [PMID: 36975379 PMCID: PMC10287150 DOI: 10.1093/jhered/esad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.
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Affiliation(s)
- Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Cinnamon Mittan-Moreau
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Madison Miller
- Savannah River Ecology Lab, University of Georgia, Aiken, SC, United States
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, United States
| | - Jessica M Judson
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
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31
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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:ani13061089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [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: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Simple Summary In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers. Abstract An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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32
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Investigating an Unknown Biodiversity: Evidence of Distinct Lineages of the Endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean. DIVERSITY 2023. [DOI: 10.3390/d15030344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Anthropogenic actions have affected marine species for a long time, through overexploitation of natural stocks and habitat degradation, influencing the life strategies of several taxa, especially rays and sharks, which have suffered significant population declines in recent years. Therefore, conservation actions and stock management have become paramount. In this regard, chola guitarfish, Pseudobatos percellens, distributed throughout the Brazilian coast, is often commercially fished by local artisanal fleets or as by-catch in shrimp trawl fisheries. Therefore, this study aimed to understand the genetic diversity of P. percellens throughout the Brazilian coast, using single nucleotide polymorphisms (SNPs). Genetic analyses employing 3329 SNPs revealed a hidden biodiversity within P. percellens, with at least one lineage occurring in the Northern and Northeastern regions and another distributed in the Southeastern/Southern Brazilian coast, with high genetic differentiation between them. However, the Discriminant Analysis of Principal Components (DAPC) indicated the presence of in fact three lineages distributed in these regions that must still be better investigated. Therefore, to ensure adequate conservation of chola guitarfish biodiversity, populations must be managed separately along the Brazilian coast. Furthermore, the need for a taxonomic review for this group is noted.
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Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Serdyukova NA, Rayko M, Bulyonkova T, Cherkasov N, Pylev V, Peterfeld V, Penin A, Balanovska E, Lapidus A, OBrien SJ, Graphodatsky A, Koepfli KP, Kliver S. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes (Basel) 2023; 14:genes14030619. [PMID: 36980891 PMCID: PMC10048373 DOI: 10.3390/genes14030619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.
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Affiliation(s)
- Aliya Yakupova
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Correspondence: (A.Y.); (A.G.)
| | - Andrey Tomarovsky
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Azamat Totikov
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Violetta Beklemisheva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Maria Logacheva
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Polina L. Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Aleksey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, 191002 Saint Petersburg, Russia
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia
| | | | - Gaik Tamazian
- Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Natalia A. Serdyukova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Mike Rayko
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Tatiana Bulyonkova
- Laboratory of Mixed Computations, A.P. Ershov Institute of Informatics Systems SB RAS, 630090 Novosibirsk, Russia
| | - Nikolay Cherkasov
- Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Vladimir Pylev
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Vladimir Peterfeld
- Baikal Branch of State Research and Industrial Center of Fisheries, 670034 Ulan-Ude, Russia
| | - Aleksey Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia
| | - Elena Balanovska
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Alla Lapidus
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - DNA Zoo Consortium
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen J. OBrien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, NOVA Southeastern University, Fort Lauderdale, FL 33004, USA
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Correspondence: (A.Y.); (A.G.)
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, 1500 Remount Road, Front Royal, VA 22630, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, 1353 Copenhagen, Denmark
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Hanko GR, Vogel MT, Negrón-Ortiz V, Moore RC. High Prevalence of Clonal Reproduction and Low Genetic Diversity in Scutellaria floridana, a Federally Threatened Florida-Endemic Mint. PLANTS (BASEL, SWITZERLAND) 2023; 12:919. [PMID: 36840267 PMCID: PMC9964081 DOI: 10.3390/plants12040919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The threatened mint Florida skullcap (Scutellaria floridana) is endemic to four counties in the Florida panhandle. Because development and habitat modification extirpated several historical occurrences, only 19 remain to date. To inform conservation management and delisting decisions, a comprehensive investigation of the genetic diversity and relatedness, population structure, and clonal diversity was conducted using SNP data generated by ddRAD. Compared with other Lamiaceae, we detected low genetic diversity (HE = 0.125-0.145), low to moderate evidence of inbreeding (FIS = -0.02-0.555), and moderate divergence (FST = 0.05-0.15). We identified eight populations with most of the genetic diversity, which should be protected in situ, and four populations with low genetic diversity and high clonality. Clonal reproduction in our circular plots and in 92% of the sites examined was substantial, with average clonal richness of 0.07 and 0.59, respectively. Scutellaria floridana appears to have experienced a continued decline in the number of extant populations since its listing under the Endangered Species Act; still, the combination of sexual and asexual reproduction may be advantageous for maintaining the viability of extant populations. However, the species will likely require ongoing monitoring, management, and increased public awareness to ensure its survival and effectively conserve its genetic diversity.
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Affiliation(s)
| | | | - Vivian Negrón-Ortiz
- Department of Biology, Miami University, Oxford, OH 45056, USA
- Florida Ecological Services Field Office, U.S. Fish and Wildlife Service, 1601 Balboa Ave., Panama City, FL 32405, USA
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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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Abstract
Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.
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Affiliation(s)
- Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Eckart Stolle
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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37
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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proc Natl Acad Sci U S A 2023; 120:e2201076120. [PMID: 36749728 PMCID: PMC9962930 DOI: 10.1073/pnas.2201076120] [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: 02/08/2023] Open
Abstract
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
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38
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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39
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Conservation genomics of an endangered arboreal mammal following the 2019-2020 Australian megafire. Sci Rep 2023; 13:480. [PMID: 36627361 PMCID: PMC9831986 DOI: 10.1038/s41598-023-27587-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The impacts of a changing climate threaten species, populations and ecosystems. Despite these significant and large-scale impacts on threatened species, many remain understudied and have little to no genetic information available. The greater glider, Petauroides volans, is an endangered species highly sensitive to the predicted changes in temperature under a changing climate and was recently severely impacted by a megafire natural disaster (85% estimated population loss). Baseline genetic data is essential for conservation management and for detecting detrimental changes in fire-effected populations. We collected genetic samples within 2 years post the 2019-2020 catastrophic Australian bushfires to examine adaptive potential, baseline genetic diversity and population structure, across their southern range in the state of New South Wales. Population genomic analyses were conducted using 8493 genome-wide SNPs for 86 greater glider individuals across 14 geographic locations. Substantial genetic structure was detected across locations, with low genetic diversity and effective population sizes observed in isolated areas. Additionally, we found signals of putative adaptation in response to temperature in greater gliders using a genotype-environment association analysis. These findings have important implications for the management of greater glider populations by identifying at-risk populations and identifying adaptive potential. We demonstrate the importance of baseline genetic information for endangered species as a practical approach to conservation. This is particularly important given the threat that changes in temperatures and megafire events, as predicted under a changing climate, poses for this species.
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40
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Thompson LM, Thurman LL, Cook CN, Beever EA, Sgrò CM, Battles A, Botero CA, Gross JE, Hall KR, Hendry AP, Hoffmann AA, Hoving C, LeDee OE, Mengelt C, Nicotra AB, Niver RA, Pérez‐Jvostov F, Quiñones RM, Schuurman GW, Schwartz MK, Szymanski J, Whiteley A. Connecting research and practice to enhance the evolutionary potential of species under climate change. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Laura M. Thompson
- U.S. Geological Survey (USGS), National Climate Adaptation Science Center and the University of Tennessee Knoxville Tennessee USA
| | | | - Carly N. Cook
- School of Biological Sciences Monash University Melbourne Australia
| | - Erik A. Beever
- USGS, Northern Rocky Mountain Science Center and Montana State University Bozeman Montana USA
| | - Carla M. Sgrò
- School of Biological Sciences Monash University Melbourne Australia
| | | | | | - John E. Gross
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | | | | | | | | | - Olivia E. LeDee
- USGS, Midwest Climate Adaptation Science Center Saint Paul Minnesota USA
| | | | | | - Robyn A. Niver
- U.S. Fish and Wildlife Service (USFWS), Branch of Listing and Policy Support Bailey's Crossroads Virginia USA
| | | | - Rebecca M. Quiñones
- Massachusetts Division of Fisheries and Wildlife Westborough Massachusetts USA
| | - Gregor W. Schuurman
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | - Michael K. Schwartz
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation Missoula Montana USA
| | - Jennifer Szymanski
- USFWS, Branch of SSA Science Support, Division of Endangered Species Onalaska Wisconsin USA
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41
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Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. CONSERV GENET 2023; 24:181-191. [PMID: 36683963 PMCID: PMC9841145 DOI: 10.1007/s10592-022-01492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, USA.,The University of Chicago, Chicago, USA
| | | | - Jessica M da Silva
- South African National Biodiversity Institute, Pretoria, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW Australia
| | - Michael J Gill
- NatureServe, Biodiversity Indicators Program, Arlington, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Francine Kershaw
- Oceans Division, Natural Resources Defense Council, NewYork, USA
| | - Robert C Lacy
- Chicago Zoological Society, Species Conservation Toolkit Initiative, Brookfield, USA
| | - Caroline Lees
- Conservation Planning Specialist Group, IUCN SSC, Auckland, New Zealand
| | | | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Australia
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Mexico City, Mexico.,Consejo Nacional de Ciencia Y Tecnología (CONACYT), Mexico City, Mexico
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Mariah H Meek
- Department of Integrative Biology; Ecology, Evolution, and Behavior Program, Michigan State University, AgBio Research, Lansing, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Katie L Millette
- Group on Earth Observations Biodiversity Observation Network (GEO BON), McGill University, Montreal, Canada
| | - Cinnamon S Mittan-Moreau
- Kellogg Biological Station; Ecology and Evolutionary Biology, Michigan State University, Lansing, USA
| | | | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, USA
| | | | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
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42
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Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti). DIVERSITY 2022. [DOI: 10.3390/d14121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.
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43
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Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review. DIVERSITY 2022. [DOI: 10.3390/d14121054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.
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44
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Meek MH, Beever EA, Barbosa S, Fitzpatrick SW, Fletcher NK, Mittan-Moreau CS, Reid BN, Campbell-Staton SC, Green NF, Hellmann JJ. Understanding Local Adaptation to Prepare Populations for Climate Change. Bioscience 2022. [DOI: 10.1093/biosci/biac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.
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Affiliation(s)
- Mariah H Meek
- Department of Integrative Biology, AgBio Research, and the Ecology, Evolution, and Behavior Program Michigan State University , East Lansing, Michigan, United States
| | - Erik A Beever
- Department of Ecology, Montana State University , Bozeman, Montana, United States
| | - Soraia Barbosa
- Department of Fish and Wildlife Sciences, University of Idaho , Moscow, Idaho, United States
| | - Sarah W Fitzpatrick
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
| | - Nicholas K Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
- Department of Biology, University of Maryland , College Park, Maryland, United States
| | - Cinnamon S Mittan-Moreau
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
| | - Brendan N Reid
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology, Evolution, and Natural Resources, Rutgers University , New Brunswick, New Jersey, United States
| | - Shane C Campbell-Staton
- Department of Ecology and Evolutionary Biology, Princeton University , Princeton, New Jersey, United States
| | - Nancy F Green
- US Fish and Wildlife Service, Falls Church , Virginia, United States
| | - Jessica J Hellmann
- Institute of the Environment and Department of Ecology, Evolution, and Behavior, University of Minnesota , Saint Paul, Minnesota, United States
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45
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High genetic diversity in American chestnut (Castanea dentata) despite a century of decline. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01473-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Srinivas Y, Yumnam B, Dutta S, Jhala Y. Assessing genetic diversity and population structure for prioritizing conservation of the critically endangered Great Indian Bustard (Aredotis nigriceps). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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47
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Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet 2022; 13:960958. [PMID: 36226192 PMCID: PMC9549127 DOI: 10.3389/fgene.2022.960958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
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Affiliation(s)
- Mirte Bosse
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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48
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Genetic structure and diversity of amphidromous sculpin in Shiretoko, a mountainous peninsula in Japan. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01472-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Holland OJ, Toomey M, Ahrens C, Hoffmann AA, Croft LJ, Sherman CDH, Miller AD. Whole genome resequencing reveals signatures of rapid selection in a virus-affected commercial fishery. Mol Ecol 2022; 31:3658-3671. [PMID: 35555938 PMCID: PMC9327721 DOI: 10.1111/mec.16499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 04/11/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Infectious diseases are recognized as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australian blacklip abalone (Haliotis rubra) following a major population crash associated with an infectious disease. Genome scans on H. rubra were performed using pooled whole genome resequencing data from commercial fishing stocks varying in historical exposure to haliotid herpesvirus-1 (HaHV-1). Approximately 25,000 single nucleotide polymorphism loci associated with virus exposure were identified, many of which mapped to genes known to contribute to HaHV-1 immunity in the New Zealand pāua (Haliotis iris) and herpesvirus response pathways in haliotids and other animal systems. These findings indicate genetic changes across a single generation in H. rubra fishing stocks decimated by HaHV-1, with stock recovery potentially determined by rapid evolutionary changes leading to virus resistance. This is a novel example of apparently rapid adaptation in natural populations of a nonmodel marine organism, highlighting the pace at which selection can potentially act to counter disease in wildlife communities.
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Affiliation(s)
- Owen J. Holland
- School of Life and Environmental SciencesDeakin UniversityWarrnamboolVictoriaAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVictoriaAustralia
| | - Madeline Toomey
- School of Life and Environmental SciencesDeakin UniversityWarrnamboolVictoriaAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVictoriaAustralia
| | - Collin Ahrens
- School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyAustralia
- Research Centre for Ecosystem ResilienceAustralian Institute of Botanical ScienceRoyal Botanic GardenSydneyNew South WalesAustralia
| | - Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Laurence J. Croft
- School of Life and Environmental SciencesDeakin UniversityWarrnamboolVictoriaAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVictoriaAustralia
| | - Craig D. H. Sherman
- School of Life and Environmental SciencesDeakin UniversityWarrnamboolVictoriaAustralia
| | - Adam D. Miller
- School of Life and Environmental SciencesDeakin UniversityWarrnamboolVictoriaAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVictoriaAustralia
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50
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Andrello M, D'Aloia C, Dalongeville A, Escalante MA, Guerrero J, Perrier C, Torres-Florez JP, Xuereb A, Manel S. Evolving spatial conservation prioritization with intraspecific genetic data. Trends Ecol Evol 2022; 37:553-564. [PMID: 35450706 DOI: 10.1016/j.tree.2022.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
Abstract
Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.
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Affiliation(s)
- Marco Andrello
- Institute for the study of Anthropic impacts and Sustainability in the marine environment, National Research Council, CNR-IAS, Rome, Italy.
| | - Cassidy D'Aloia
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jimena Guerrero
- Sociedad Científica de Investigación Transdisciplinaria y Especialización (SCITE), Calimaya, México
| | - Charles Perrier
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade, Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Santos, Brazil
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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