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Smith CE, Gilby BL, van de Merwe J, Jones J, Tait H, Townsend KA. Predictive modelling reveals Australian continental risk hotspots for marine debris interactions with key threatened species. GLOBAL CHANGE BIOLOGY 2024; 30:e17313. [PMID: 38837834 DOI: 10.1111/gcb.17313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 06/07/2024]
Abstract
Anthropogenic debris is a global threat that impacts threatened species through various lethal and sub-lethal consequences, as well as overall ecosystem health. This study used a database of over 24,000 beach surveys of marine debris collated by the Australian Marine Debris Initiative from 2012 to 2021, with two key objectives: (1) identify variables that most influence the occurrence of debris hotspots on a continental scale and (2) use these findings to identify likely hotspots of interaction between threatened species and marine debris. The number of particles found in each beach survey was modelled alongside fifteen biological, social, and physical spatial variables including land use, physical oceanography, population, rainfall, distance to waste facilities, ports, and mangroves to identify the significant drivers of debris deposition. The model of best fit for predicting debris particle abundance was calculated using a generalized additive model. Overall, debris was more abundant at sites near catchments with high annual rainfall (mm), intensive land use (km2), and that were nearer to ports (km) and mangroves (km). These results support previous studies which state that mangroves are a significant sink for marine debris, and that large ports and urbanized catchments are significant sources for marine debris. We illustrate the applicability of these models by quantifying significant overlap between debris hotspots and the distributions for four internationally listed threatened species that exhibit debris interactions; green turtle (26,868 km2), dugong (16,164 km2), Australian sea lion (2903 km2) and Flesh-footed Shearwater (2413 km2). This equates to less than 1% (Flesh-footed Shearwater, Australian sea lion), over 2% (green sea turtle) and over 5% (dugong) of their habitat being identified as areas of high risk for marine debris interactions. The results of this study hold practical value, informing decision-making processes, managing debris pollution at continental scales, as well as identifying gaps in species monitoring.
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Affiliation(s)
- Caitlin E Smith
- School of Science, Technology and Engineering, University of the Sunshine Coast, Hervey Bay, Queensland, Australia
| | - Ben L Gilby
- School of Science, Technology and Engineering, University of the Sunshine Coast, Petrie, Queensland, Australia
| | - Jason van de Merwe
- Australian Rivers Institute, Griffith University, Southport, Queensland, Australia
| | - Jodi Jones
- Tangaroa Blue Foundation, Australian Marine Debris Initiative Database, Dunsborough, Western Australia, Australia
| | - Heidi Tait
- Tangaroa Blue Foundation, Australian Marine Debris Initiative Database, Dunsborough, Western Australia, Australia
| | - Kathy A Townsend
- School of Science, Technology and Engineering, University of the Sunshine Coast, Hervey Bay, Queensland, Australia
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Izaguirre-Toriz V, Aguirre-Liguori JA, Latorre-Cárdenas MC, Arima EY, González-Rodríguez A. Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán. Mol Ecol 2024:e17424. [PMID: 38813851 DOI: 10.1111/mec.17424] [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: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
Climate change and land use change are two main drivers of global biodiversity decline, decreasing the genetic diversity that populations harbour and altering patterns of local adaptation. Landscape genomics allows measuring the effect of these anthropogenic disturbances on the adaptation of populations. However, both factors have rarely been considered simultaneously. Based on a set of 3660 SNPs from which 130 were identified as outliers by a genome-environment association analysis (LFMM), we modelled the spatial turnover of allele frequencies in 19 localities of Pinus leiophylla across the Avocado Belt in Michoacán state, Mexico. Then, we evaluated the effect of climate change and land use change scenarios, in addition to evaluating assisted gene flow strategies and connectivity metrics across the landscape to identify priority conservation areas for the species. We found that localities in the centre-east of the Avocado Belt would be more vulnerable to climate change, while localities in the western area are more threatened by land conversion to avocado orchards. Assisted gene flow actions could aid in mitigating both threats. Connectivity patterns among forest patches will also be modified by future habitat loss, with central and eastern parts of the Avocado Belt maintaining the highest connectivity. These results suggest that areas with the highest priority for conservation are in the eastern part of the Avocado Belt, including the Monarch Butterfly Biosphere Reserve. This work is useful as a framework that incorporates distinct layers of information to provide a more robust representation of the response of tree populations to anthropogenic disturbances.
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Affiliation(s)
- Vanessa Izaguirre-Toriz
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria), Coyoacán, Mexico
| | - Jonás A Aguirre-Liguori
- Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - María Camila Latorre-Cárdenas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Eugenio Y Arima
- Department of Geography and the Environment, University of Texas at Austin, Austin, Texas, USA
| | - Antonio González-Rodríguez
- Laboratorio Nacional de Innovación Ecotecnológica Para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM Campus Morelia, Morelia, Mexico
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Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor MI, Wong MC. Variation in genomic vulnerability to climate change across temperate populations of eelgrass ( Zostera marina). Evol Appl 2024; 17:e13671. [PMID: 38650965 PMCID: PMC11033490 DOI: 10.1111/eva.13671] [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: 01/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 04/25/2024] Open
Abstract
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole-genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterize population structure, gene flow and environmental associations of 23 eelgrass populations ranging from the Northeast United States to Atlantic, subarctic and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise F ST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be potentially more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Benedikte Vercaemer
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries CentreSt. John'sNewfoundland and LabradorCanada
| | - France Dufresne
- Département de BiologieUniversité du Québec à RimouskiRimouskiQuebecCanada
| | - Fanny Noisette
- Institut des Sciences de la mer, Université du Québec à RimouskiRimouskiQuebecCanada
| | - Mary I. O'Connor
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Melisa C. Wong
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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Chen Y, Gao Y, Huang X, Li S, Zhang Z, Zhan A. Incorporating adaptive genomic variation into predictive models for invasion risk assessment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 18:100299. [PMID: 37701243 PMCID: PMC10494315 DOI: 10.1016/j.ese.2023.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Global climate change is expected to accelerate biological invasions, necessitating accurate risk forecasting and management strategies. However, current invasion risk assessments often overlook adaptive genomic variation, which plays a significant role in the persistence and expansion of invasive populations. Here we used Molgula manhattensis, a highly invasive ascidian, as a model to assess its invasion risks along Chinese coasts under climate change. Through population genomics analyses, we identified two genetic clusters, the north and south clusters, based on geographic distributions. To predict invasion risks, we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability, respectively. These approaches yielded distinct predictions: the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster (i.e., lower invasion risks), while the species distribution model indicated higher future habitat suitability for the same cluster (i.e, higher invasion risks). By integrating these models, we found that the south cluster exhibited minor genome-niche disruptions in the future, indicating higher invasion risks. Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change. Moreover, incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yangchun Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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Layton KKS, Brieuc MSO, Castilho R, Diaz-Arce N, Estévez-Barcia D, Fonseca VG, Fuentes-Pardo AP, Jeffery NW, Jiménez-Mena B, Junge C, Kaufmann J, Leinonen T, Maes SM, McGinnity P, Reed TE, Reisser CMO, Silva G, Vasemägi A, Bradbury IR. Predicting the future of our oceans-Evaluating genomic forecasting approaches in marine species. GLOBAL CHANGE BIOLOGY 2024; 30:e17236. [PMID: 38519845 DOI: 10.1111/gcb.17236] [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: 12/18/2023] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 03/25/2024]
Abstract
Climate change is restructuring biodiversity on multiple scales and there is a pressing need to understand the downstream ecological and genomic consequences of this change. Recent advancements in the field of eco-evolutionary genomics have sought to include evolutionary processes in forecasting species' responses to climate change (e.g., genomic offset), but to date, much of this work has focused on terrestrial species. Coastal and offshore species, and the fisheries they support, may be even more vulnerable to climate change than their terrestrial counterparts, warranting a critical appraisal of these approaches in marine systems. First, we synthesize knowledge about the genomic basis of adaptation in marine species, and then we discuss the few examples where genomic forecasting has been applied in marine systems. Next, we identify the key challenges in validating genomic offset estimates in marine species, and we advocate for the inclusion of historical sampling data and hindcasting in the validation phase. Lastly, we describe a workflow to guide marine managers in incorporating these predictions into the decision-making process.
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Affiliation(s)
- K K S Layton
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - R Castilho
- University of the Algarve, Faro, Portugal
- Centre for Marine Sciences, University of the Algarve, Faro, Portugal
- Pattern Institute, Faro, Portugal
| | - N Diaz-Arce
- AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - D Estévez-Barcia
- Department of Fish and Shellfish, Greenland Institute of Natural Resources, Nuuk, Greenland
| | - V G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - A P Fuentes-Pardo
- Department of Immunology, Genetics and Pathology, SciLifeLab Data Centre, Uppsala University, Uppsala, Sweden
| | - N W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - B Jiménez-Mena
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - C Junge
- Institute of Marine Research, Tromso, Norway
| | | | - T Leinonen
- Natural Resources Institute Finland, Helsinki, Finland
| | - S M Maes
- Flanders Research Institute for Agriculture, Fisheries and Food, Ostend, Belgium
| | - P McGinnity
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - T E Reed
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - C M O Reisser
- MARBEC, University of Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - G Silva
- MARE-Marine and Environmental Sciences Centre/ARNET-Aquatic Research Network, ISPA-Instituto Universitário, Lisbon, Portugal
| | - A Vasemägi
- Swedish University of Agricultural Sciences, Drottningholm, Sweden
- Estonian University of Life Sciences, Tartu, Estonia
| | - I R Bradbury
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
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6
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Ruan T, Wei W, Zhang Z, Zhou H. Research on the Changes in Distribution and Habitat Suitability of the Chinese Red Panda Population. Animals (Basel) 2024; 14:424. [PMID: 38338067 PMCID: PMC10854785 DOI: 10.3390/ani14030424] [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: 12/17/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The study of the dynamics of species habitat is of great significance for maintaining or adjusting the current habitat protection management strategy. However, the current research on the Chinese red panda's habitat is limited to the analysis of a single period, which makes it difficult to quantify the changes in its habitat on a temporal scale and greatly hinders the formulation of the overall protection and management strategies that are to be used for the Chinese red panda. This study simulated habitat suitability at different temporal scales to quantify the trend of changes in habitat quality and analyzed the reasons for the changes in habitat suitability in certain regions. The results showed that the overall suitability of the Chinese red panda's habitat increased and that the area of suitable habitats expanded. Suitable Chinese red panda habitats in the mountains of Qionglai (1662.73 km2), Daxiangling (230.30 km2), Xiaoxiangling (549.47 km2), and Liangshan (50.39 km2) increased by a total of 2452.89 km2. The suitability of habitats in the central part of the Liangshan Mountains has declined significantly, which is positively correlated with changes in temperature seasonality (BIO4, R = 0.18) and negatively correlated with changes in annual average temperature (BIO1, R = -0.03) as well as changes in the proportion of farmland (FARMLAND, R = -0.14). The local extinction of isolated populations of Chinese red pandas in the Minshan Mountains is the main factor leading to their distribution retreat rather than a decrease in habitat quality. The research results help us to provide a scientific basis for the formulation of conservation and management strategies for Chinese red pandas at different scales.
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Affiliation(s)
- Tao Ruan
- College of Giant Panda, China West Normal University, Nanchong 637009, China; (T.R.); (W.W.); (Z.Z.)
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province, Nanchong 637009, China
| | - Wei Wei
- College of Giant Panda, China West Normal University, Nanchong 637009, China; (T.R.); (W.W.); (Z.Z.)
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province, Nanchong 637009, China
| | - Zejun Zhang
- College of Giant Panda, China West Normal University, Nanchong 637009, China; (T.R.); (W.W.); (Z.Z.)
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province, Nanchong 637009, China
| | - Hong Zhou
- College of Giant Panda, China West Normal University, Nanchong 637009, China; (T.R.); (W.W.); (Z.Z.)
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province, Nanchong 637009, China
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Ding C, Newbold T, Ameca EI. Assessing the global vulnerability of dryland birds to heatwaves. GLOBAL CHANGE BIOLOGY 2024; 30:e17136. [PMID: 38273501 DOI: 10.1111/gcb.17136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
As global average surface temperature increases, extreme climatic events such as heatwaves are becoming more frequent and intense, which can drive biodiversity responses such as rapid population declines and/or shifts in species distributions and even local extirpations. However, the impacts of extreme climatic events are largely ignored in conservation plans. Birds are known to be susceptible to heatwaves, especially in dryland ecosystems. Understanding which birds are most vulnerable to heatwaves, and where these birds occur, can offer a scientific basis for adaptive management and conservation. We assessed the relative vulnerability of 1196 dryland bird species to heatwaves using a trait-based approach. Among them, 888 bird species are estimated to be vulnerable to heatwaves (170 highly vulnerable, eight extremely vulnerable), of which ~91% are currently considered non-threatened by the IUCN, which suggests that many species will likely become newly threatened with intensifying climate change. We identified the top three hotspot areas of heatwave-vulnerable species in Australia (208 species), Southern Africa (125 species) and Eastern Africa (99 species). Populations of vulnerable species recorded in the Living Planet Database were found to be declining significantly faster than those of non-vulnerable species (p = .048) after heatwaves occurred. In contrast, no significant difference in population trends between vulnerable and non-vulnerable species was detected when no heatwave occurred (p = .34). This suggests that our vulnerability framework correctly identified vulnerable species and that heatwaves are already impacting the population trends of these species. Our findings will help prioritize heatwave-vulnerable birds in dryland ecosystems in risk mitigation and adaptation management as the frequency of heatwaves accelerates in the coming decades.
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Affiliation(s)
- Chenchen Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Tim Newbold
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Eric I Ameca
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Climate Change Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Gland, Switzerland
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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [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: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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9
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Zhang L, Zhang YY, Ma LX, Dong YW. Evaluation of species thermal sensitivity with individual-based physiological performance. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106212. [PMID: 37812948 DOI: 10.1016/j.marenvres.2023.106212] [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: 06/04/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Ignoring intraspecific variations can prevent us from accurately assessing species' thermal sensitivity to global warming. Individual-based physiological performance provides a feasible solution to depict species' thermal sensitivity using a bottom-up approach. We measured the cardiac performance of intertidal bivalves (1159 individuals from multiple populations of six bivalves), determined the upper thermal limit of each individual, calculated the proportions of individuals suffering sublethal/lethal heat stress, and mapped sensitive regions to high temperatures. Results showed that high inter-individual variations of physiological performance existed in levels of populations and species, and species' thermal sensitivity was positively related to the intraspecific variations of heat tolerance. This bottom-up approach scaled up from individual, population to species emphasizes the importance of individual-based physiology performance in assessing thermal sensitivity across different hierarchical levels and enables better evaluating and forecasting of species responses to global warming.
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Affiliation(s)
- Liang Zhang
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Yu-Yang Zhang
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Lin-Xuan Ma
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Yun-Wei Dong
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China.
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10
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Mendoza-Portillo V, García-De León FJ, von der Heyden S. Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish. GLOBAL CHANGE BIOLOGY 2023; 29:4107-4125. [PMID: 37078996 DOI: 10.1111/gcb.16732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
The responses of marine species to environmental changes and anthropogenic pressures (e.g., fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Using a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. The contemporary genomic structure showed three populations-two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects on fisheries that depend on this resource.
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Affiliation(s)
- Verónica Mendoza-Portillo
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- School of Climate Studies, Stellenbosch University, Matieland, South Africa
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Song WH, Li JJ. The effects of intraspecific variation on forecasts of species range shifts under climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159513. [PMID: 36257416 DOI: 10.1016/j.scitotenv.2022.159513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
As global climate change is altering the distribution range of macroalgae across the globe, it is critical to assess its impact on species range shifts to inform the biodiversity conservation of macroalgae. Latitude/environmental gradients could cause intraspecific variability, which may result in distinct responses to climate change. It remains unclear whether geographical variation occurs in the response of species' populations to climate change. We tested this assumption using the brown alga Sargassum thunbergii, a habitat-forming macroalgae encompassing multiple divergent lineages along the Northwest Pacific. Previous studies revealed a distinct lineage of S. thunbergii in rear-edge populations. Given the phylogeographic structure and temperature gradients, we divided these populations into the southern and northern groups. We assessed the physiological responses of the two groups to temperature changes and estimated their niche differences using n-dimensional hypervolumes. A higher photosynthetic rate and antioxidative abilities were detected in the southern group of S. thunbergii than in the northern group. In addition, significant niche differentiation was detected between the two groups, suggesting the possibility for local adaptation. Given these results, we inferred that the southern group (rear-edge populations) may be more resilient to climate change. To examine climate-driven range shifts of S. thunbergii, we constructed species- and lineage-level species distribution models (SDMs). Predictions of both levels showed considerable distribution contracts along the Chinese coasts in the future. For the southern group, the lineage-level model predicted less habitat loss than the species-level model. Our results highlight the importance of considering intraspecific variation in climate change vulnerability assessments for coastal species.
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Affiliation(s)
- Wang-Hui Song
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China
| | - Jing-Jing Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing 210024, China.
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12
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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13
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DeSaix MG, George TL, Seglund AE, Spellman GM, Zavaleta ES, Ruegg KC. Forecasting climate change response in an alpine specialist songbird reveals the importance of considering novel climate. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Matthew G. DeSaix
- Department of Biology Colorado State University Fort Collins Colorado USA
| | - T. Luke George
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado USA
| | | | - Garth M. Spellman
- Department of Zoology Denver Museum of Nature and Science Denver Colorado USA
| | - Erika S. Zavaleta
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins Colorado USA
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14
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Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). GLOBAL CHANGE BIOLOGY 2022; 28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.
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Affiliation(s)
- Rémi Tournebize
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Leyli Borner
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- INRAE, Le Rheu, France
| | - Stéphanie Manel
- CEFE, CNRS, EPHE-PSL University, IRD, Univ Montpellier, Montpellier, France
| | - Christine N Meynard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Yves Vigouroux
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
| | | | - Coralie Fournier
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- School of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Kassam
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- Danone Nutricia Research, Singapore
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
| | | | - Hugues Parrinello
- CNRS, INSERM, Univ. Montpellier, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | | | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | | | | | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Valérie Poncet
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
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15
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Dalongeville A, Nielsen ES, Teske PR, Heyden S. Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Erica S. Nielsen
- Department of Evolution and Ecology University of California, Davis Davis California USA
| | - Peter R. Teske
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Auckland Park South Africa
| | - Sophie Heyden
- Department of Botany and Zoology Evolutionary Genomics Group Stellenbosch University Stellenbosch South Africa
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Boulanger E, Benestan L, Guerin PE, Dalongeville A, Mouillot D, Manel S. Climate differently influences the genomic patterns of two sympatric marine fish species. J Anim Ecol 2021; 91:1180-1195. [PMID: 34716929 DOI: 10.1111/1365-2656.13623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022]
Abstract
Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographical scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers capable of revealing climatic-associated genetic variations. We explored how space, dispersal and environment shape the genomic patterns of two sympatric fish species in the Mediterranean Sea, which ranks among the oceanic basins most affected by climate change and human pressure. We hypothesized that the population structure and climate-associated genomic signatures of selection would be stronger in the less mobile species, as restricted gene flow tends to facilitate the fixation of locally adapted alleles. To test our hypothesis, we genotyped two species with contrasting dispersal abilities: the white seabream Diplodus sargus and the striped red mullet Mullus surmuletus. We collected 823 individuals and used genotyping by sequencing (GBS) to detect 8,206 single nucleotide polymorphisms (SNPs) for the seabream and 2,794 for the mullet. For each species, we identified highly differentiated genomic regions (i.e. outliers) and disentangled the relative contribution of space, dispersal and environmental variables (climate, marine primary productivity) on the outliers' genetic structure to test the prevalence of gene flow and local adaptation. We observed contrasting patterns of gene flow and adaptive genetic variation between the two species. The seabream showed a distinct Alboran sea population and panmixia across the Mediterranean Sea. The mullet revealed additional differentiation within the Mediterranean Sea that was significantly correlated to summer and winter temperatures, as well as marine primary productivity. Functional annotation of the climate-associated outlier SNPs then identified candidate genes involved in heat tolerance that could be examined to further predict species' responses to climate change. Our results illustrate the key steps of a comparative seascape genomics study aiming to unravel the evolutionary processes at play in marine species, to better anticipate their response to climate change. Defining population adaptation capacities and environmental niches can then serve to incorporate evolutionary processes into species conservation planning.
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Affiliation(s)
- Emilie Boulanger
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France.,MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Laura Benestan
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Pierre-Edouard Guerin
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | - David Mouillot
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Institut Universitaire de France, Paris, France
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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