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Lott MJ, Frankham GJ, Eldridge MDB, Alquezar‐Planas DE, Donnelly L, Zenger KR, Leigh KA, Kjeldsen SR, Field MA, Lemon J, Lunney D, Crowther MS, Krockenberger MB, Fisher M, Neaves LE. Reversing the decline of threatened koala ( Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 2024; 14:e11700. [PMID: 39091325 PMCID: PMC11289790 DOI: 10.1002/ece3.11700] [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: 02/05/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.
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Affiliation(s)
- Matthew J. Lott
- Australian Museum Research InstituteSydneyNew South WalesAustralia
| | | | | | | | - Lily Donnelly
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kellie A. Leigh
- Science for Wildlife LtdMount VictoriaNew South WalesAustralia
| | - Shannon R. Kjeldsen
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
- Immunogenomics LabGarvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - John Lemon
- JML Environmental ConsultantsArmidaleNew South WalesAustralia
- School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNew South WalesAustralia
| | - Daniel Lunney
- Australian Museum Research InstituteSydneyNew South WalesAustralia
- Department of Planning and EnvironmentParramattaNew South WalesAustralia
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mathew S. Crowther
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark B. Krockenberger
- Sydney School of Veterinary ScienceUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark Fisher
- 3D Ecology MappingEmerald BeachNew South WalesAustralia
| | - Linda E. Neaves
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
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2
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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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3
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Alvanou MV, Loukovitis D, Kyritsi S, Apostolidis AP, Michaelidis B, Giantsis IA. Genetic prospective of a local invader: the strange pattern of Pontastacus leptodactylus population structure in Greece and Turkey based on microsatellite DNA. Mol Biol Rep 2024; 51:765. [PMID: 38874834 DOI: 10.1007/s11033-024-09696-y] [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: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The combination of the increasing demand of freshwater crayfish exports, the reduced population sizes due to overfishing, the crayfish plague epidemics and the habitat degradation, have led to unrecorded translocations of Pontastacus leptodactylus in Greek lakes. METHODS AND RESULTS In the present study, the genetics of five narrow clawed crayfish (P. leptodactylus) populations were studied, namely three translocated populations inhabiting in Northern Greece, one native Greek population from Evros river and one potential progeny source population from Turkey. Nine microsatellite loci previously designed for the specific species were investigated, in order to assess the levels of genetic diversity and further to confirm the origin of these translocated populations some decades after the translocation events. Our results confirmed that the source population for the translocated Greek population is the Turkish lake Eğirdir. Further, despite the low values of the number of alleles, heterozygosity, and FST the populations were generally diverse, providing evidence for local adaptation. CONCLUSIONS The low values of FIS for the translocated populations in combination with the high values of gene flow, possibly indicate the existence of re-introducing events. Apart from the translocated populations, high levels of genetic diversity and heterozygosity were observed in Evros population, suggesting it as a possible unit for future conservation purposes both as a donor population for reintroduction purposes as well as a unique gene pool protection source. To the best of our knowledge this is the first study dealing with the genetic composition of Greek P. leptodactylus populations from Nothern Greece, operating as a first step towards the development of proper management practices for restocking events and monitoring of translocated populations.
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Affiliation(s)
- Maria V Alvanou
- Division of Animal Science, Faculty of Agricultural Science, University of Western Macedonia, Florina, 53100, Greece
| | - Dimitrios Loukovitis
- Department of Fisheries and Aquaculture, School of Agricultural Sciences, University of Patras, Messolonghi, 30200, Greece
| | - Stavroula Kyritsi
- Department of Agriculture, International Hellenic University, Sindos, Thessaloniki, Greece
| | - Apostolos P Apostolidis
- Laboratory of Ichthyology & Fisheries, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Ioannis A Giantsis
- Division of Animal Science, Faculty of Agricultural Science, University of Western Macedonia, Florina, 53100, Greece.
- Laboratory of Ichthyology & Fisheries, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
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4
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Huang JP, Wu SP, Chen WY, Pham GJ, Kuan YH. Genomic data revealed inbreeding despite a geographically connected stable effective population size since the Holocene in the protected Formosan Long-Arm Scarab beetle, Cheirotonus formosanus. J Hered 2024; 115:292-301. [PMID: 38364316 DOI: 10.1093/jhered/esae006] [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: 11/18/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies.
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Affiliation(s)
- Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Ping Wu
- Department of Earth and Life Science, University of Taipei, Taipei, Taiwan
| | - Wei-Yun Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Guan Jie Pham
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Al Hikmani H, van Oosterhout C, Birley T, Labisko J, Jackson HA, Spalton A, Tollington S, Groombridge JJ. Can genetic rescue help save Arabia's last big cat? Evol Appl 2024; 17:e13701. [PMID: 38784837 PMCID: PMC11113348 DOI: 10.1111/eva.13701] [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: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.
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Affiliation(s)
- Hadi Al Hikmani
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Office for Conservation of the EnvironmentDiwan of Royal CourtMuscatOman
- The Royal Commission for AlUlaAlUlaSaudi Arabia
| | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Thomas Birley
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Centre for Biodiversity and Environment Research, Research Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Island Biodiversity and Conservation CentreUniversity of SeychellesVictoriaSeychelles
- Department of Life SciencesThe Natural History MuseumLondonUK
| | - Hazel A. Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
| | | | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- School of Animal Rural and Environmental SciencesNottingham Trent UniversityNottinghamUK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [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: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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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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Otalora K, Riera JL, Tavecchia G, Rotger A, Igual JM, Trotta JP, Baldo L. Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data. Ecol Evol 2024; 14:e11407. [PMID: 38799398 PMCID: PMC11116764 DOI: 10.1002/ece3.11407] [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: 03/01/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.
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Affiliation(s)
- Katherin Otalora
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Fundación FUNMAJO, EBA, RAIEC, Biodiversity BranchTunjaBoyacáColombia
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Andreu Rotger
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - José Manuel Igual
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Jean‐Remi Paul Trotta
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Institute for Research on Biodiversity (IRBio)University of Barcelona (UB)BarcelonaSpain
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9
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Tengstedt ANB, Liu S, Jacobsen MW, Gundlund C, Møller PR, Berg S, Bekkevold D, Hansen MM. Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.). Mol Ecol 2024:e17367. [PMID: 38686435 DOI: 10.1111/mec.17367] [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: 01/25/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Population genomics analysis holds great potential for informing conservation of endangered populations. We focused on a controversial case of European whitefish (Coregonus spp.) populations. The endangered North Sea houting is the only coregonid fish that tolerates oceanic salinities and was previously considered a species (C. oxyrhinchus) distinct from European lake whitefish (C. lavaretus). However, no firm evidence for genetic-based salinity adaptation has been available. Also, studies based on microsatellite and mitogenome data suggested surprisingly recent divergence (c. 2500 years bp) between houting and lake whitefish. These data types furthermore have provided no evidence for possible inbreeding. Finally, a controversial taxonomic revision recently classified all whitefish in the region as C. maraena, calling conservation priorities of houting into question. We used whole-genome and ddRAD sequencing to analyse six lake whitefish populations and the only extant indigenous houting population. Demographic inference indicated post-glacial expansion and divergence between lake whitefish and houting occurring not long after the Last Glaciation, implying deeper population histories than previous analyses. Runs of homozygosity analysis suggested not only high inbreeding (FROH up to 30.6%) in some freshwater populations but also FROH up to 10.6% in the houting prompting conservation concerns. Finally, outlier scans provided evidence for adaptation to high salinities in the houting. Applying a framework for defining conservation units based on current and historical reproductive isolation and adaptive divergence led us to recommend that the houting be treated as a separate conservation unit regardless of species status. In total, the results underscore the potential of genomics to inform conservation practices, in this case clarifying conservation units and highlighting populations of concern.
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Affiliation(s)
| | - Shenglin Liu
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Magnus W Jacobsen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Søren Berg
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
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10
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Pisciottano F, Campos MC, Penna C, Bruque CD, Gabaldón T, Saragüeta P. Positive selection in gamete interaction proteins in Carnivora. Mol Ecol 2024; 33:e17263. [PMID: 38318732 DOI: 10.1111/mec.17263] [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: 06/28/2022] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The absence of robust interspecific isolation barriers among pantherines, including the iconic South American jaguar (Panthera onca), led us to study molecular evolution of typically rapidly evolving reproductive proteins within this subfamily and related groups. In this study, we delved into the evolutionary forces acting on the zona pellucida (ZP) gamete interaction protein family and the sperm-oocyte fusion protein pair IZUMO1-JUNO across the Carnivora order, distinguishing between Caniformia and Feliformia suborders and anticipating few significant diversifying changes in the Pantherinae subfamily. A chromosome-resolved jaguar genome assembly facilitated coding sequences, enabling the reconstruction of protein evolutionary histories. Examining sequence variability across more than 30 Carnivora species revealed that Feliformia exhibited significantly lower diversity compared to its sister taxa, Caniformia. Molecular evolution analyses of ZP2 and ZP3, subunits directly involved in sperm-recognition, unveiled diversifying positive selection in Feliformia, Caniformia and Pantherinae, although no significant changes were linked to sperm binding. Structural cross-linking ZP subunits, ZP4 and ZP1 exhibited lower levels or complete absence of positive selection. Notably, the fusion protein IZUMO1 displayed prominent positive selection signatures and sites in basal lineages of both Caniformia and Feliformia, extending along the Caniformia subtree but absent in Pantherinae. Conversely, JUNO did not exhibit any positive selection signatures across tested lineages and clades. Eight Caniformia-specific positive selected sites in IZUMO1 were detected within two JUNO-interaction clusters. Our findings provide for the first time insights into the evolutionary trajectories of ZP proteins and the IZUMO1-JUNO gamete interaction pair within the Carnivora order.
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Affiliation(s)
- Francisco Pisciottano
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - María Clara Campos
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - Clementina Penna
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - Carlos David Bruque
- Unidad de Conocimiento Traslacional Hospitalaria Patagónica, Hospital de Alta Complejidad El Calafate SAMIC, El Calafate, Santa Cruz, Argentina
| | - Toni Gabaldón
- Barcelona Supercomputing Center (BSC), Institute for Research in Biomedicine (IRB), and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Patricia Saragüeta
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
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11
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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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12
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Quigley KM. Breeding and Selecting Corals Resilient to Global Warming. Annu Rev Anim Biosci 2024; 12:209-332. [PMID: 37931139 DOI: 10.1146/annurev-animal-021122-093315] [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: 11/08/2023]
Abstract
Selective breeding of resilient organisms is an emerging topic in marine conservation. It can help us predict how species will adapt in the future and how we can help restore struggling populations effectively in the present. Scleractinian corals represent a potential tractable model system given their widescale phenotypic plasticity across fitness-related traits and a reproductive life history based on mass synchronized spawning. Here, I explore the justification for breeding in corals, identify underutilized pathways of acclimation, and highlight avenues for quantitative targeted breeding from the coral host and symbiont perspective. Specifically, the facilitation of enhanced heat tolerance by targeted breeding of plasticity mechanisms is underutilized. Evidence from theoretical genetics identifies potential pitfalls, including inattention to physical and genetic characteristics of the receiving environment. Three criteria for breeding emerge from this synthesis: selection from warm, variable reefs that have survived disturbance. This information will be essential to protect what we have and restore what we can.
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Affiliation(s)
- K M Quigley
- The Minderoo Foundation, Perth, Western Australia, Australia;
- James Cook University, Townsville, Queensland, Australia
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13
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Parker LM, Scanes E, O'Connor WA, Dove M, Elizur A, Pörtner HO, Ross PM. Resilience against the impacts of climate change in an ecologically and economically significant native oyster. MARINE POLLUTION BULLETIN 2024; 198:115788. [PMID: 38056289 DOI: 10.1016/j.marpolbul.2023.115788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023]
Abstract
Climate change is acidifying and warming our oceans, at an unprecedented rate posing a challenge for marine invertebrates vital across the globe for ecological services and food security. Here we show it is possible for resilience to climate change in an ecologically and economically significant oyster without detrimental effects to the energy budget. We exposed 24 pair-mated genetically distinct families of the Sydney rock oyster, Saccostrea glomerata to ocean acidification and warming for 4w and measured their resilience. Resilience was identified as the capacity to defend their acid-base balance without a loss of energy available for Scope for Growth (SFG). Of the 24 families, 13 were better able to defend their acid-base balance while eight had no loss of energy availability with a positive SFG. This study has found oyster families with reslience against climate change without a loss of SFG, is an essential mitigation strategy, in a critical mollusc.
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Affiliation(s)
- Laura M Parker
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Elliot Scanes
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Sydney, New South Wales 2006, Australia; Climate Change Cluster, University of Technology, Ultimo, Sydney, New South Wales 2007, Australia
| | - Wayne A O'Connor
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Michael Dove
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Abigail Elizur
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Hans-Otto Pörtner
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven 27570, Germany
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Sydney, New South Wales 2006, Australia.
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14
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Jordan R, Harrison PA, Breed M. The eco-evolutionary risks of not changing seed provenancing practices in changing environments. Ecol Lett 2024; 27:e14348. [PMID: 38288869 DOI: 10.1111/ele.14348] [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: 06/01/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 02/01/2024]
Abstract
Sourcing seed from local populations has been the long-standing default for native restoration plantings for numerous eco-evolutionary reasons. However, rapidly changing environments are revealing risks associated with both non-local and local provenancing. As alternative strategies gain interest, we argue to progress seed sourcing discussions towards developing risk-based decision-making that weighs the risks of changing and not changing in a changing environment, transcending historic default positions and local versus non-local debates.
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Affiliation(s)
| | - Peter A Harrison
- Australian Research Council Centre for Forest Value & School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Martin Breed
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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15
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Hoste A, Capblancq T, Broquet T, Denoyelle L, Perrier C, Buzan E, Šprem N, Corlatti L, Crestanello B, Hauffe HC, Pellissier L, Yannic G. Projection of current and future distribution of adaptive genetic units in an alpine ungulate. Heredity (Edinb) 2024; 132:54-66. [PMID: 38082151 PMCID: PMC10798982 DOI: 10.1038/s41437-023-00661-2] [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: 07/14/2022] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/21/2024] Open
Abstract
Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.
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Affiliation(s)
- Amélie Hoste
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Thibaut Capblancq
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Thomas Broquet
- CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Charles Perrier
- UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000, Zagreb, Croatia
| | - Luca Corlatti
- Stelvio National Park - ERSAF Lombardia, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Barbara Crestanello
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Loïc Pellissier
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zrich, Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Glenn Yannic
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
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16
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Cook CN, Redford KH, Schwartz MW. Species conservation in the era of genomic science. Bioscience 2023; 73:885-890. [PMID: 38162573 PMCID: PMC10755706 DOI: 10.1093/biosci/biad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024] Open
Abstract
The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.
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Affiliation(s)
- Carly N Cook
- Monash University's School of Biological Sciences, Melbourne, Australia
| | - Kent H Redford
- University of New England's Department of Environmental Studies, Biddeford, Maine, United States
| | - Mark W Schwartz
- Department of Environmental Science and Policy, University of California, Davis, Davis, California, United States
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17
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Black JG, van Rooyen ARJ, Heinze D, Gaffney R, Hoffmann AA, Schmidt TL, Weeks AR. Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii). Mol Ecol 2023. [PMID: 38013623 DOI: 10.1111/mec.17224] [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: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Identifying and analysing isolated populations is critical for conservation. Isolation can make populations vulnerable to local extinction due to increased genetic drift and inbreeding, both of which should leave imprints of decreased genome-wide heterozygosity. While decreases in heterozygosity among populations are frequently investigated, fewer studies have analysed how heterozygosity varies among individuals, including whether heterozygosity varies geographically along lines of discrete population structure or with continuous patterns analogous to isolation by distance. Here we explore geographical patterns of differentiation and individual heterozygosity in the threatened eastern barred bandicoot (Perameles gunnii) in Tasmania, Australia, using genomic data from 85 samples collected between 2008 and 2011. Our analyses identified two isolated demes undergoing significant genetic drift, and several areas of fine-scale differentiation across Tasmania. We observed discrete genetic structures across geographical barriers and continuous patterns of isolation by distance, with little evidence of recent or historical migration. Using a recently developed analytical pipeline for estimating autosomal heterozygosity, we found individual heterozygosities varied within demes by up to a factor of two, and demes with low-heterozygosity individuals also still contained those with high heterozygosity. Spatial interpolation of heterozygosity scores clarified these patterns and identified the isolated Tasman Peninsula as a location where low-heterozygosity individuals were more common than elsewhere. Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualised metric for identifying source animals for translocation.
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Affiliation(s)
- John G Black
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Dean Heinze
- Research Centre of Applied Alpine Ecology, La Trobe University, Melbourne, Victoria, Australia
| | - Robbie Gaffney
- Department of Natural Resources and Environment, Hobart, Tasmania, Australia
| | - Ary A Hoffmann
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas L Schmidt
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew R Weeks
- School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
- Cesar Australia, Brunswick, Victoria, Australia
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18
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Nimbs MJ, Champion C, Lobos SE, Malcolm HA, Miller AD, Seinor K, Smith SD, Knott N, Wheeler D, Coleman MA. Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change. PeerJ 2023; 11:e16498. [PMID: 38025735 PMCID: PMC10676721 DOI: 10.7717/peerj.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.
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Affiliation(s)
- Matt J. Nimbs
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Curtis Champion
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Simon E. Lobos
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Hamish A. Malcolm
- NSW Department of Primary Industries, Fisheries Research, Coffs Harbour, NSW, Australia
| | - Adam D. Miller
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Kate Seinor
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Stephen D.A. Smith
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Aquamarine Australia, Mullaway, NSW, Australia
| | - Nathan Knott
- NSW Department of Primary Industries, Fisheries Research, Huskisson, NSW, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange, NSW, Australia
| | - Melinda A. Coleman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
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19
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Zhu BR, Zhang XY, Yang XX, Liao WJ. Development of polymorphic microsatellite markers for Fagus pashanica (Fagaceae) using next-generation sequencing. Genes Genet Syst 2023; 98:277-281. [PMID: 37880102 DOI: 10.1266/ggs.23-00160] [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: 10/27/2023] Open
Abstract
Fagus pashanica is an endangered and endemic tree species in China. To understand its genetic diversity and structure for effective conservation, we used next-generation sequencing data to develop a set of microsatellite markers. Twenty-three of the 68 designed loci were successfully amplified. Fifteen polymorphic loci with clear peaks were selected for further analyses in three F. pashanica populations sampled from Nanjiang, Wangcang and Pingwu counties in Sichuan Province, China. The number of alleles per locus ranged from two to 11. The levels of observed and expected heterozygosity ranged from 0.033-0.852 and 0.033-0.787, respectively. All 23 loci were also successfully amplified in F. longipetiolata and F. lucida, and 19 were successfully amplified in F. engleriana. These microsatellite markers will be useful for population genetic studies of F. pashanica and other Fagus species.
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Affiliation(s)
- Bi-Ru Zhu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University
| | - Xiao-Ya Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University
| | - Xiao-Xi Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University
- Xinyuan School
| | - Wan-Jin Liao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University
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20
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Wu R, Qi J, Li W, Wang L, Shen Y, Liu J, Teng Y, Roos C, Li M. Landscape genomics analysis provides insights into future climate change-driven risk in rhesus macaque. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165746. [PMID: 37495138 DOI: 10.1016/j.scitotenv.2023.165746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/01/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]
Abstract
Climate change significantly affects the suitability of wildlife habitats. Thus, understanding how animals adapt ecologically and genetically to climate change is important for targeted species protection. Rhesus macaques (Macaca mulatta) are widely distributed and multi-climatically adapted primates. This study explored how rhesus macaques adapt to climate change by integrating ecological and genetic methods and applying species distribution models (SDMs) and a gradient forest (GF) model. The findings suggested that temperature seasonality primarily affects habitat suitability and indicated that climate change will have a dramatic impact on macaque populations in the future. We also applied genotype-environment association (GEA) analyses and selection signature analyses to identify genes associated with climate change and provide possible explanations for the adaptation of rhesus macaques to climatic environments. The population genomics analyses suggested that the Taihang population has the highest genomic vulnerability with inbreeding and low heterozygosity. Combined with the higher ecological vulnerability, additional conservation strategies are required for this population under higher risk of climate change. Our work measured the impact of climate change and enabled the identification of populations that exhibit high vulnerability to severe climate change. Such information is useful for selecting populations of rhesus macaques as subject of long-term monitoring or evolutionary rescue under future climate change.
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Affiliation(s)
- Ruifeng Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Teng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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21
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de Jong M, van Rensburg AJ, Whiteford S, Yung CJ, Beaumont M, Jiggins C, Bridle J. Rapid evolution of novel biotic interactions in the UK Brown Argus butterfly uses genomic variation from across its geographical range. Mol Ecol 2023; 32:5742-5756. [PMID: 37800849 DOI: 10.1111/mec.17138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023]
Abstract
Understanding the rate and extent to which populations can adapt to novel environments at their ecological margins is fundamental to predicting the persistence of biological communities during ongoing and rapid global change. Recent range expansion in response to climate change in the UK butterfly Aricia agestis is associated with the evolution of novel interactions with a larval food plant, and the loss of its ability to use an ancestral host species. Using ddRAD analysis of 61,210 variable SNPs from 261 females from throughout the UK range of this species, we identify genomic regions at multiple chromosomes that are associated with evolutionary responses, and their association with demographic history and ecological variation. Gene flow appears widespread throughout the range, despite the apparently fragmented nature of the habitats used by this species. Patterns of haplotype variation between selected and neutral genomic regions suggest that evolution associated with climate adaptation is polygenic, resulting from the independent spread of alleles throughout the established range of this species, rather than the colonization of pre-adapted genotypes from coastal populations. These data suggest that rapid responses to climate change do not depend on the availability of pre-adapted genotypes. Instead, the evolution of novel forms of biotic interaction in A. agestis has occurred during range expansion, through the assembly of novel genotypes from alleles from multiple localities.
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Affiliation(s)
- Maaike de Jong
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alexandra Jansen van Rensburg
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Samuel Whiteford
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Carl J Yung
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Chris Jiggins
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jon Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
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22
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O’Brien P, Carr N, Bowman J. Using sentinel nodes to evaluate changing connectivity in a protected area network. PeerJ 2023; 11:e16333. [PMID: 37901466 PMCID: PMC10612492 DOI: 10.7717/peerj.16333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/30/2023] [Indexed: 10/31/2023] Open
Abstract
It has been recognized that well-connected networks of protected areas are needed to halt the continued loss of global biodiversity. The recently signed Kunming-Montreal biodiversity agreement commits countries to protecting 30% of terrestrial lands in well-connected networks of protected areas by 2030. To meet these ambitious targets, land-use planners and conservation practitioners will require tools to identify areas important for connectivity and track future changes. In this study we present methods using circuit theoretic models with a subset of sentinel park nodes to evaluate connectivity for a protected areas network. We assigned a lower cost to natural areas within protected areas, under the assumption that animal movement within parks should be less costly given the regulation of activities. We found that by using mean pairwise effective resistance (MPER) as an indicator of overall network connectivity, we were able to detect changes in a parks network in response to simulated land-use changes. As expected, MPER increased with the addition of high-cost developments and decreased with the addition of new, low-cost protected areas. We tested our sentinel node method by evaluating connectivity for the protected area network in the province of Ontario, Canada. We also calculated a node isolation index, which highlighted differences in protected area connectivity between the north and the south of the province. Our method can help provide protected areas ecologists and planners with baseline estimates of connectivity for a given protected area network and an indicator that can be used to track changes in connectivity in the future.
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Affiliation(s)
- Paul O’Brien
- Ontario Ministry of Natural Resources and Forestry (MNRF), Peterborough, Ontario, Canada
| | - Natasha Carr
- Ontario Ministry of the Environment, Conservation and Parks (MECP), Peterborough, Ontario, Canada
| | - Jeff Bowman
- Ontario Ministry of Natural Resources and Forestry (MNRF), Peterborough, Ontario, Canada
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23
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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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24
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Fiesinger A, Held C, Melzner F, Putchim L, Reusch TBH, Schmidt AL, Wall M. Population genetic differentiation of the ubiquitous brooding coral Pocillopora acuta along Phuket Island reefs in the Andaman Sea, Thailand. BMC Ecol Evol 2023; 23:42. [PMID: 37626296 PMCID: PMC10464487 DOI: 10.1186/s12862-023-02153-7] [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: 03/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The widespread Indo-Pacific coral species Pocillopora acuta Lamarck, 1816 displays varying levels of asexual versus sexual reproduction, with strong repercussions on genetic diversity, connectivity and genetic structuring within and among populations. For many geographic regions, baseline information on genetic diversity is still lacking, particularly in the Andaman Sea. The region suffered a massive heat-induced bleaching event in 2010 with high coral cover loss of branching coral species such as P. acuta. A subsequent bleaching in 2016, however, revealed a mild bleaching response in pocilloporids compared to other coral taxa in the region, suggesting that rare, heat tolerant genotypes had been selected by the 2010 bleaching event. In order to test whether this potential 'evolutionary rescue' event has led to a low genetic diversity, we conducted a population genetic survey covering a total of nine different P. acuta populations (336 individuals) along a 50 km coastal stretch around Phuket Island, Thailand. We used six microsatellite markers to assess genotypic diversity and to determine the prevalent mode of reproduction (i.e. sexual or asexual recruitment). RESULTS In contrast to other Indian Ocean P. acuta populations, the majority of corals in this study adopted a sexual reproduction mode (75% across all populations). At the same time, substantial regional gene flow was observed around Phuket Island with strong genetic differentiation as indicated by three genetic clusters that were separated by only a few kilometers. Patterns of isolation by distance over 0.7 - 40 km suggest small-scale genetic barriers, such as changing currents throughout each monsoonal season, potentially contributing to locally restricted dispersal of P. acuta larvae. CONCLUSIONS The occurrence of distinct genetic clusters within short coastal stretches suggests that the 2010 bleaching event has not led to extreme genetic impoverishment. While more in-depth genomic analyses are necessary to investigate changes in genetic diversity following extreme bleaching events, our results will help guide conservation efforts to maintain genetic diversity of a coral species that likely will be dominant in future, warmer Andaman Sea reefs.
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Affiliation(s)
- Anna Fiesinger
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany.
- Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78464, Germany.
| | - Christoph Held
- Alfred-Wegener-Institut, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Lalita Putchim
- Phuket Marine Biological Centre, Wichit, Phuket, Mueang Phukt District, 83000, Thailand
| | - Thorsten B H Reusch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine Evolutionary Ecoloy, Wischhofstraße 1-3, Kiel, 24148, Germany
| | - Andrea L Schmidt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany
- Cooperative Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Marlene Wall
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany.
- Alfred-Wegener-Institut, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany.
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25
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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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26
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Putra AR, Yen JDL, Fournier-Level A. Forecasting trait responses in novel environments to aid seed provenancing under climate change. Mol Ecol Resour 2023; 23:565-580. [PMID: 36308465 DOI: 10.1111/1755-0998.13728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/28/2022]
Abstract
Revegetation projects face the major challenge of sourcing optimal plant material. This is often done with limited information about plant performance and increasingly requires factoring resilience to climate change. Functional traits can be used as quantitative indices of plant performance and guide seed provenancing, but trait values expected under novel conditions are often unknown. To support climate-resilient provenancing efforts, we develop a trait prediction model that integrates the effect of genetic variation with fine-scale temperature variation. We train our model on multiple field plantings of Arabidopsis thaliana and predict two relevant fitness traits-days-to-bolting and fecundity-across the species' European range. Prediction accuracy was high for days-to-bolting and moderate for fecundity, with the majority of trait variation explained by temperature differences between plantings. Projection under future climate predicted a decline in fecundity, although this response was heterogeneous across the range. In response, we identified novel genotypes that could be introduced to genetically offset the fitness decay. Our study highlights the value of predictive models to aid seed provenancing and improve the success of revegetation projects.
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Affiliation(s)
- Andhika R Putra
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jian D L Yen
- Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
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27
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Dauphin B, Rellstab C, Wüest RO, Karger DN, Holderegger R, Gugerli F, Manel S. Re-thinking the environment in landscape genomics. Trends Ecol Evol 2023; 38:261-274. [PMID: 36402651 DOI: 10.1016/j.tree.2022.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022]
Abstract
Detecting the extrinsic selective pressures shaping genomic variation is critical for a better understanding of adaptation and for forecasting evolutionary responses of natural populations to changing environmental conditions. With increasing availability of geo-referenced environmental data, landscape genomics provides unprecedented insights into how genomic variation and underlying gene functions affect traits potentially under selection. Yet, the robustness of genotype-environment associations used in landscape genomics remains tempered due to various limitations, including the characteristics of environmental data used, sampling designs employed, and statistical frameworks applied. Here, we argue that using complementary or new environmental data sources and well-informed sampling designs may help improve the detection of selective pressures underlying patterns of local adaptation in various organisms and environments.
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Affiliation(s)
- Benjamin Dauphin
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland.
| | | | - Rafael O Wüest
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Dirk N Karger
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; Institute of Integrative Biology (IBZ), ETH, Zurich, 8092 Zurich, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Stéphanie Manel
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland; CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, 34000 Montpellier, France; Institut Universitaire de France, Paris, France
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28
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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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29
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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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30
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Young MA, Critchell K, Miller AD, Treml EA, Sams M, Carvalho R, Ierodiaconou D. Mapping the impacts of multiple stressors on the decline in kelps along the coast of Victoria, Australia. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mary A. Young
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Warrnambool Vic. Australia
| | - Kay Critchell
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Queenscliff Vic. Australia
| | - Adam D. Miller
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Warrnambool Vic. Australia
| | - Eric A. Treml
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Queenscliff Vic. Australia
| | - Michael Sams
- Parks Victoria, Marine and Coastal Science and Programs Melbourne Vic. Australia
| | - Rafael Carvalho
- School of Earth, Atmosphere and Environment Monash University Melbourne Vic. Australia
| | - Daniel Ierodiaconou
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Warrnambool Vic. Australia
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31
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Mijangos JL, Bino G, Hawke T, Kolomyjec SH, Kingsford RT, Sidhu H, Grant T, Day J, Dias KN, Gongora J, Sherwin WB. Fragmentation by major dams and implications for the future viability of platypus populations. Commun Biol 2022; 5:1127. [PMID: 36329312 PMCID: PMC9633709 DOI: 10.1038/s42003-022-04038-9] [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: 03/16/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
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Affiliation(s)
- Jose L. Mijangos
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia ,grid.1039.b0000 0004 0385 7472Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Gilad Bino
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Tahneal Hawke
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Stephen H. Kolomyjec
- grid.258898.60000 0004 0462 9201College of Science and the Environment, Lake Superior State University, Sault Sainte Marie, USA
| | - Richard T. Kingsford
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Harvinder Sidhu
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia
| | - Tom Grant
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Jenna Day
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Kimberly N. Dias
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Jaime Gongora
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - William B. Sherwin
- grid.1005.40000 0004 4902 0432Evolution & Ecology Research Centre, UNSW, Sydney, Australia
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32
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Strong bidirectional gene flow between fish lineages separated for over 100,000 years. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01476-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractRestoring levels of genetic diversity in small and declining populations is increasingly being considered in biodiversity conservation. Evidence-based genetic management requires assessment of risks and benefits of crossing populations. Because risks are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation of lineages. However, the paucity of empirical datasets on fitness consequences of longer separation times tends to favour crossing lineages with conservatively short separations, restricting wildlife managers’ options. Here, we assessed the genetic outcomes of interbreeding in the wild between lineages of a threatened Australian freshwater fish (Macquarie perch) separated by an estimated 119,000–385,000 years of evolution in distinct environments. Fish belonging to the Murray-Darling Basin (MDB) lineage escaped from Cataract Dam—into which they were translocated in ~ 1915—into the Cataract River, where they interbred with the local Hawkesbury-Nepean Basin (HNB) lineage. Analyses of reduced-representation genomic data revealed no evidence of genetic incompatibilities during interbreeding of the two lineages in the Cataract River: assignment to genotypic clusters indicated a spectrum of hybrid types including second generation hybrids and backcrosses to both parental lineages. Thus, no adverse effects were detected from genetic mixing of populations separated by > 100,000 years. We are not advocating purposely crossing the two lineages for management purposes under present cost–benefit considerations, because there are currently sufficient intra-lineage source populations to beneficially mix. Instead, this study presents a useful calibration point: two morphologically different lineages evolved in different habitats for 119,000–385,000 years can successfully interbreed.
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33
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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] [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
- *Correspondence: Mirte Bosse,
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Beet CR, Hogg ID, Cary SC, McDonald IR, Sinclair BJ. The Resilience of Polar Collembola (Springtails) in a Changing Climate. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100046. [PMID: 36683955 PMCID: PMC9846479 DOI: 10.1016/j.cris.2022.100046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/30/2022] [Accepted: 09/08/2022] [Indexed: 06/17/2023]
Abstract
Assessing the resilience of polar biota to climate change is essential for predicting the effects of changing environmental conditions for ecosystems. Collembola are abundant in terrestrial polar ecosystems and are integral to food-webs and soil nutrient cycling. Using available literature, we consider resistance (genetic diversity; behavioural avoidance and physiological tolerances; biotic interactions) and recovery potential for polar Collembola. Polar Collembola have high levels of genetic diversity, considerable capacity for behavioural avoidance, wide thermal tolerance ranges, physiological plasticity, generalist-opportunistic feeding habits and broad ecological niches. The biggest threats to the ongoing resistance of polar Collembola are increasing levels of dispersal (gene flow), increased mean and extreme temperatures, drought, changing biotic interactions, and the arrival and spread of invasive species. If resistance capacities are insufficient, numerous studies have highlighted that while some species can recover from disturbances quickly, complete community-level recovery is exceedingly slow. Species dwelling deeper in the soil profile may be less able to resist climate change and may not recover in ecologically realistic timescales given the current rate of climate change. Ultimately, diverse communities are more likely to have species or populations that are able to resist or recover from disturbances. While much of the Arctic has comparatively high levels of diversity and phenotypic plasticity; areas of Antarctica have extremely low levels of diversity and are potentially much more vulnerable to climate change.
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Affiliation(s)
- Clare R. Beet
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian D. Hogg
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - S. Craig Cary
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua - School of Science, Te Whare Wānanga o Waikato - University of Waikato, Hamilton, New Zealand
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Brent J. Sinclair
- Department of Biology, University of Western Ontario, London, ON, Canada
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Leaf Economic and Hydraulic Traits Signal Disparate Climate Adaptation Patterns in Two Co-Occurring Woodland Eucalypts. PLANTS 2022; 11:plants11141846. [PMID: 35890479 PMCID: PMC9320154 DOI: 10.3390/plants11141846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 11/23/2022]
Abstract
With climate change impacting trees worldwide, enhancing adaptation capacity has become an important goal of provenance translocation strategies for forestry, ecological renovation, and biodiversity conservation. Given that not every species can be studied in detail, it is important to understand the extent to which climate adaptation patterns can be generalised across species, in terms of the selective agents and traits involved. We here compare patterns of genetic-based population (co)variation in leaf economic and hydraulic traits, climate–trait associations, and genomic differentiation of two widespread tree species (Eucalyptus pauciflora and E. ovata). We studied 2-year-old trees growing in a common-garden trial established with progeny from populations of both species, pair-sampled from 22 localities across their overlapping native distribution in Tasmania, Australia. Despite originating from the same climatic gradients, the species differed in their levels of population variance and trait covariance, patterns of population variation within each species were uncorrelated, and the species had different climate–trait associations. Further, the pattern of genomic differentiation among populations was uncorrelated between species, and population differentiation in leaf traits was mostly uncorrelated with genomic differentiation. We discuss hypotheses to explain this decoupling of patterns and propose that the choice of seed provenances for climate-based plantings needs to account for multiple dimensions of climate change unless species-specific information is available.
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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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vonHoldt BM, Hinton JW, Shutt AC, Murphy SM, Karlin ML, Adams JR, Waits LP, Brzeski KE. Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf. SCIENCE ADVANCES 2022; 8:eabn7731. [PMID: 35767623 PMCID: PMC9242586 DOI: 10.1126/sciadv.abn7731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana. We detected that 38 to 62% of the coyote genomes contained red wolf ancestry acquired in the past 30 years and have an admixture profile similar to that of the canids captured before the extirpation of red wolves. We further documented a positive correlation between ancestry and weight. Our findings highlight the importance of hybrids and admixed genomes as a reservoir of endangered species ancestry for innovative conservation efforts. Together, this work presents an unprecedented system that conservation can leverage to enrich the recovery program of an endangered species.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | | | - Sean M. Murphy
- Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - Melissa L. Karlin
- Department of Physics and Environmental Science, St. Mary’s University, San Antonio, TX, USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin E. Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, MI, USA
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Lancaster LT, Fuller ZL, Berger D, Barbour MA, Jentoft S, Wellenreuther M. Understanding climate change response in the age of genomics. J Anim Ecol 2022; 91:1056-1063. [PMID: 35668551 DOI: 10.1111/1365-2656.13711] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - David Berger
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Matthew A Barbour
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Evans MJ, Weeks AR, Scheele BC, Gordon IJ, Neaves LE, Andrewartha TA, Brockett B, Rapley S, Smith KJ, Wilson BA, Manning AD. Coexistence conservation: Reconciling threatened species and invasive predators through adaptive ecological and evolutionary approaches. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Maldwyn J. Evans
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
| | - Andrew R. Weeks
- School of BioSciences The University of Melbourne Parkville Victoria Australia
| | - Ben C. Scheele
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Iain J. Gordon
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
- The James Hutton Institute Dundee UK
- Central Queensland University Townsville Queensland Australia
- Land & water, CSIRO Townsville Queensland Australia
- Lead, Protected Places Mission, National Environmental Science Program Reef and Rainforest Research Centre Cairns Queensland Australia
| | - Linda E. Neaves
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Tim A. Andrewartha
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Brittany Brockett
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Shoshana Rapley
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Kiarrah J. Smith
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Belinda A. Wilson
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
| | - Adrian D. Manning
- Fenner School of Environment and Society The Australian National University Canberra Australian Capital Territory Australia
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Massatti R, Winkler DE. Spatially explicit management of genetic diversity using ancestry probability surfaces. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rob Massatti
- US Geological Survey, Southwest Biological Science Center Flagstaff AZ USA
| | - Daniel E. Winkler
- US Geological Survey, Southwest Biological Science Center Tucson AZ USA
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Wolf Dispersal Patterns in the Italian Alps and Implications for Wildlife Diseases Spreading. Animals (Basel) 2022; 12:ani12101260. [PMID: 35625106 PMCID: PMC9137635 DOI: 10.3390/ani12101260] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. For many species, little is known about dispersal, despite its importance to conservation. We documented the natural dispersal processes of an expanding wolf (Canis lupus) population in the Italian Alps to understand the dynamics of the recolonization pattern and identify diseases that might be connected with the process through the use of non-invasive genetic sampling over a 20-year period. By documenting 55 dispersal events, with an average minimum straight dispersal distance of 65.8 km (±67.7 km), from 7.7 km to 517.2 km, we discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading. Abstract Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. Despite its importance to conservation, little is known about dispersal for several species. Dispersal processes in expanding wolf (Canis lupus) populations in Europe is not well documented. Documenting the natural dispersal pattern of the expanding wolf population in the Alps might help understanding the overall population dynamics and identifying diseases that might be connected with the process. We documented 55 natural dispersal events of the expanding Italian wolf alpine population over a 20-year period through the use of non-invasive genetic sampling. We examined a 16-locus microsatellite DNA dataset of 2857 wolf samples mainly collected in the Western Alps. From this, we identified 915 individuals, recaptured 387 (42.3%) of individuals, documenting 55 dispersal events. On average, the minimum straight dispersal distance was 65.8 km (±67.7 km), from 7.7 km to 517.2 km. We discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.
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Jørgensen DB, Ørsted M, Kristensen TN. Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster. J Evol Biol 2022; 35:868-878. [PMID: 35532930 PMCID: PMC9325394 DOI: 10.1111/jeb.14015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affect behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour-a locomotor response used to measure, e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared with the locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4 . Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.
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Affiliation(s)
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg E, Denmark.,Department of Biology, Aarhus University, Aarhus C, Denmark
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Woolridge CB, Fant JB, Flores AI, Schultz K, Kramer AT. Variation in overall fitness due to seed source: projections for predictive provenancing. Restor Ecol 2022. [DOI: 10.1111/rec.13717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher B. Woolridge
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden Glencoe IL USA
- Plant Biology and Conservation Program Northwestern University Evanston IL USA
| | - Jeremie B. Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden Glencoe IL USA
- Plant Biology and Conservation Program Northwestern University Evanston IL USA
| | - Ana I. Flores
- School of Life Sciences University of Hawai'i at Mānoa Honolulu HI USA
| | | | - Andrea T. Kramer
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden Glencoe IL USA
- Plant Biology and Conservation Program Northwestern University Evanston IL USA
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Gutiérrez-Reinoso MA, Aponte PM, García-Herreros M. A review of inbreeding depression in dairy cattle: current status, emerging control strategies, and future prospects. J DAIRY RES 2022; 89:1-10. [PMID: 35225176 DOI: 10.1017/s0022029922000188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Dairy cattle breeding has historically focused on relatively small numbers of elite bulls as sires of sons. In recent years, even if generation intervals were reduced and more diverse sires of sons could have been selected, genomic selection has not fundamentally changed the fact that a large number of individuals are being analyzed. However, a relatively small number of elite bulls are still siring those animals. Therefore inbreeding-derived negative consequences in the gene pool have brought concern. The detrimental effects of non-additive genetic changes such as inbreeding depression and dominance have been widely disseminated while seriously affecting bioeconomically important parameters because of an antagonistic relationship between dairy production and reproductive traits. Therefore, the estimation of benefits and limitations of inbreeding and variance of the selection response deserves to be evaluated and discussed to preserve genetic variability, a significant concern in the selection of individuals for reproduction and production. Short-term strategies for genetic merit improvement through modern breeding programs have severely lowered high-producing dairy cattle fertility potential. Since the current selection programs potentially increase long-term costs, genetic diversity has decreased globally as a consequence. Therefore, a greater understanding of the potential that selection programs have for supporting long-term genetic sustainability and genetic diversity among dairy cattle populations should be prioritized in managing farm profitability. The present review provides a broad approach to current inbreeding-derived problems, identifying critical points to be solved and possible alternative strategies to control selection against homozygous haplotypes while maintaining sustained selection pressure. Moreover, this manuscript explores future perspectives, emphasizing theoretical applications and critical points, and strategies to avoid the adverse effects of inbreeding in dairy cattle. Finally, this review provides an overview of challenges that will soon require multidisciplinary approaches to managing dairy cattle populations, intending to combine increases in productive trait phenotypes with improvements in reproductive, health, welfare, linear conformation, and adaptability traits into the foreseeable future.
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Affiliation(s)
- Miguel A Gutiérrez-Reinoso
- Universidad Técnica de Cotopaxi, Facultad de Ciencias Agropecuarias y Recursos Naturales, Carrera de Medicina Veterinaria (UTC), Latacunga, Ecuador
- Laboratorio de Biotecnología Animal, Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán (UdeC), Chile
| | - Pedro M Aponte
- Universidad San Francisco de Quito (USFQ), Colegio de Ciencias Biológicas y Ambientales (COCIBA), Campus Cumbayá, Quito, Ecuador
- Instituto de Investigaciones en Biomedicina, iBioMed, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito, Ecuador
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Willi Y, Kristensen TN, Sgrò CM, Weeks AR, Ørsted M, Hoffmann AA. Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proc Natl Acad Sci U S A 2022; 119:e2105076119. [PMID: 34930821 PMCID: PMC8740573 DOI: 10.1073/pnas.2105076119] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Torsten N Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew R Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Cesar Australia, Brunswick, VIC 3056, Australia
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
- Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia;
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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Harrison PA, Davidson NJ, Bailey TG, Jones M, Gilfedder L, Bridle K, Bowman DMJS, Baker TP, Richardson BJ, Wallis L, Potts BM. A decade of restoring a temperate woodland: Lessons learned and future directions. ECOLOGICAL MANAGEMENT & RESTORATION 2021. [DOI: 10.1111/emr.12537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, Nigam P, Zachariah A, Jhala YV, Kardos M, Ramakrishnan U. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc Natl Acad Sci U S A 2021; 118:e2023018118. [PMID: 34848534 PMCID: PMC8670471 DOI: 10.1073/pnas.2023018118] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 01/03/2023] Open
Abstract
Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.
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Affiliation(s)
- Anubhab Khan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Kaushalkumar Patel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Harsh Shukla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ashwin Viswanathan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Nature Conservation Foundation, Mysore 570017, India
| | | | | | - Parag Nigam
- Wildlife Institute of India, Dehradun 248001, India
| | | | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112;
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- Department of Biotechnology-Wellcome Trust India Alliance, Hyderabad 500034, India
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Holland OJ, Young MA, Sherman CDH, Tan MH, Gorfine H, Matthews T, Miller AD. Ocean warming threatens key trophic interactions supporting a commercial fishery in a climate change hotspot. GLOBAL CHANGE BIOLOGY 2021; 27:6498-6511. [PMID: 34529873 DOI: 10.1111/gcb.15889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Worldwide, rising ocean temperatures are causing declines and range shifts in marine species. The direct effects of climate change on the biology of marine organisms are often well documented; yet, knowledge on the indirect effects, particularly through trophic interactions, is largely lacking. We provide evidence of ocean warming decoupling critical trophic interactions supporting a commercially important mollusc in a climate change hotspot. Dietary assessments of the Australian blacklip abalone (Haliotis rubra) indicate primary dependency on a widespread macroalgal species (Phyllospora comosa) which we show to be in state of decline due to ocean warming, resulting in abalone biomass reductions. Niche models suggest further declines in P. comosa over the coming decades and ongoing risks to H. rubra. This study highlights the importance of studies from climate change hotspots and understanding the interplay between climate and trophic interactions when determining the likely response of marine species to environmental changes.
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Affiliation(s)
- Owen J Holland
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Mary A Young
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Mun Hua Tan
- School of Biosciences, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Harry Gorfine
- School of Biosciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Ty Matthews
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
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Westergaard KB, Kyrkjeeide MO, Brandrud MK. Using genomics to guide seed-sourcing at the right taxonomical level for ecological restoration projects: The complex case of Carex bigelowii s.lat. in Norway. Ecol Evol 2021; 11:17117-17131. [PMID: 34938497 PMCID: PMC8668773 DOI: 10.1002/ece3.8350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
There is a growing demand for ecological restoration using suitable seeds following international standards or national legal demands for local seed-sourcing. However, before selecting the appropriate geographic origin of seeds, it is vital to explore taxonomic complexity related to the focal taxa. We used ddRAD-seq to screen genomic diversity within Carex bigelowii s.lat. focussing on Norway. This species complex is considered a candidate for seeding, but presents considerable morphological, ecological, and genetic variation. The genetic structure of 132 individuals of C. bigelowii s.lat., including Carex nigra as an outgroup, was explored using ordinations, clustering analyses, and a genetic barrier algorithm. Two highly divergent clusters were evident, supporting the recognition of two taxonomic units "C. dacica" and C. bigelowii "subsp. bigelowii". Previously defined seed-sourcing regions for C. bigelowii s.lat. did not consider the known taxonomic complexity, and therefore interpreted the overall genetic structure as seed-sourcing regions, not taxa. We estimated genetic neighborhood sizes within each taxon to be 100-150 km and 300 km, respectively, indicating species-specific delimitations of local seed-sourcing regions. Frequent hybrids, local genetic distinctiveness, and suggested ecotypes add complexity to the discussed seed-sourcing regions. Our results show how genomic screening of diversity and structure in a species complex can alleviate the taxonomic impediment, inform practical questions, and legal requirements related to seed-sourcing, and together with traditional taxonomic work provide necessary information for a sound management of biodiversity.
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