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Kvalnes T, Flagstad Ø, Våge J, Strand O, Viljugrein H, Sæther B. Harvest and decimation affect genetic drift and the effective population size in wild reindeer. Evol Appl 2024; 17:e13684. [PMID: 38617828 PMCID: PMC11009432 DOI: 10.1111/eva.13684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/29/2024] [Accepted: 03/13/2024] [Indexed: 04/16/2024] Open
Abstract
Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N e) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N e of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N e/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14 years period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2% in 2005-2018 and 44.8% in 2021). Increased harvest rates decreased N e in the simulations, but less sex biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N e. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to a disease will also depend on population impacts of the disease and how these interact with management actions.
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Affiliation(s)
- Thomas Kvalnes
- Norwegian Institute for Nature Research (NINA)TrondheimNorway
- Centre for Biodiversity Dynamics (CBD), Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | | | - Jørn Våge
- Norwegian Veterinary InstituteÅsNorway
| | - Olav Strand
- Norwegian Institute for Nature Research (NINA)TrondheimNorway
| | | | - Bernt‐Erik Sæther
- Centre for Biodiversity Dynamics (CBD), Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Gjærevoll Center for Biodiversity Foresight AnalysesNorwegian University of Science and Technology (NTNU)TrondheimNorway
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2
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Miettinen A, Romakkaniemi A, Dannewitz J, Pakarinen T, Palm S, Persson L, Östergren J, Primmer CR, Pritchard VL. Temporal allele frequency changes in large-effect loci reveal potential fishing impacts on salmon life-history diversity. Evol Appl 2024; 17:e13690. [PMID: 38681510 PMCID: PMC11046039 DOI: 10.1111/eva.13690] [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: 08/15/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Fishing has the potential to influence the life-history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large-effect loci linked with ecologically important life-history traits, such as age at maturity in Atlantic salmon (Salmo salar), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93-year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping-by-sequencing approach (GT-seq), we discovered strong within-season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within-season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life-history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life-history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature.
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Affiliation(s)
- Antti Miettinen
- Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | | | - Johan Dannewitz
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | | | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | - Lo Persson
- Department of Wildlife, Fish and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Johan Östergren
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | - Craig R. Primmer
- Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Victoria L. Pritchard
- Institute for Biodiversity & Freshwater ConservationUniversity of the Highlands & IslandsInvernessUK
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3
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Grzegorczyk E, Caizergues A, Eraud C, Francesiaz C, Le Rest K, Guillemain M. Demographic and evolutionary consequences of hunting of wild birds. Biol Rev Camb Philos Soc 2024. [PMID: 38409953 DOI: 10.1111/brv.13069] [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: 10/27/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
Hunting has a long tradition in human evolutionary history and remains a common leisure activity or an important source of food. Herein, we first briefly review the literature on the demographic consequences of hunting and associated analytical methods. We then address the question of potential selective hunting and its possible genetic/evolutionary consequences. Birds have historically been popular models for demographic studies, and the huge amount of census and ringing data accumulated over the last century has paved the way for research about the demographic effects of harvesting. By contrast, the literature on the evolutionary consequences of harvesting is dominated by studies on mammals (especially ungulates) and fish. In these taxa, individuals selected for harvest often have particular traits such as large body size or extravagant secondary sexual characters (e.g. antlers, horns, etc.). Our review shows that targeting individuals according to such genetically heritable traits can exert strong selective pressures and alter the evolutionary trajectory of populations for these or correlated traits. Studies focusing on the evolutionary consequences of hunting in birds are extremely rare, likely because birds within populations appear much more similar, and do not display individual differences to the same extent as many mammals and fishes. Nevertheless, even without conscious choice by hunters, there remains the potential for selection through hunting in birds, for example by genetically inherited traits such as personality or pace-of-life. We emphasise that because so many bird species experience high hunting pressure, the possible selective effect of harvest in birds and its evolutionary consequences deserves far more attention, and that hunting may be one major driver of bird evolutionary trajectories that should be carefully considered in wildlife management schemes.
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Affiliation(s)
- Emilienne Grzegorczyk
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 405 Route de Prissé-la-Charrière, Villiers-en-Bois, 79360, France
| | - Alain Caizergues
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 08 Bd A. Einstein, CS42355, Nantes Cedex 3, 44323, France
| | - Cyril Eraud
- Office Français de la Biodiversité, Service Conservation et Gestion des Espèces à Enjeux, 405 Route de Prissé-la-Charrière, Villiers-en-Bois, 79360, France
| | - Charlotte Francesiaz
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 147 Avenue de Lodève, Juvignac, 34990, France
| | - Kévin Le Rest
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, 08 Bd A. Einstein, CS42355, Nantes Cedex 3, 44323, France
| | - Matthieu Guillemain
- Office Français de la Biodiversité, Service Conservation et Gestion Durable des Espèces Exploitées, La Tour du Valat, Le Sambuc, Arles, 13200, France
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4
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Cusson P, Pelletier F. Individual behaviour, growth, survival and vulnerability to hunting in a large mammal. Ecol Evol 2024; 14:e11003. [PMID: 38352198 PMCID: PMC10862178 DOI: 10.1002/ece3.11003] [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: 12/22/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
Humans have exploited wild animals for thousands of years. Recent studies indicate that harvest-induced selection on life-history and morphological traits may lead to ecological and evolutionary changes. Less attention has been given to harvest-induced selection on behavioural traits, especially in terrestrial systems. We assessed in a wild population of large terrestrial mammals whether decades of hunting led to harvest-induced selection on trappability, a proxy of risk-taking behaviour. We investigated links between trappability, horn growth and survival across individuals in early life and quantified the correlations between early-life trappability and horn growth with availability to hunters and probability of being shot. We found positive among-individual correlations between early-life trappability and horn growth, early-life trappability and survival and early-life horn growth and survival. Faster growing individuals were more likely to be available to hunters and shot at a young age. We found no correlations between early-life trappability and availability to hunters or probability of being shot. Our results show that correlations between behaviour and growth can occur in wild terrestrial population but may be context dependent. This result highlights the difficulty in formulating general predictions about harvest-induced selection on behaviour, which can be affected by species ecology, harvesting regulations and harvesting methods used. Future studies should investigate mechanisms linking physiological, behavioural and morphological traits and how this effects harvest vulnerability to evaluate the potential for harvest to drive selection on behaviour in wild animal populations.
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Affiliation(s)
| | - Fanie Pelletier
- Département de BiologieUniversité de SherbrookeSherbrookeQuébecCanada
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5
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [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: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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6
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Sánchez-Murrieta E, Macías-Duarte A, Castillo-Gámez RA, Varela-Romero A, Montoya AB, Weaver JH, Pacheco-Hoyos NG. Genetic variability and population structure of the Montezuma quail ( Cyrtonyx montezumae) in the northern limit of its distribution. PeerJ 2023; 11:e16585. [PMID: 38089905 PMCID: PMC10712304 DOI: 10.7717/peerj.16585] [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: 04/14/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Restricted movement among populations decreases genetic variation, which may be the case for the Montezuma quail (Cyrtonyx montezumae), a small game bird that rarely flies long distances. In the northern limit of its distribution, it inhabits oak-juniper-pine savannas of Arizona, New Mexico, and Texas. Understanding genetic structure can provide information about the demographic history of populations that is also important for conservation and management. The objective of this study was to determine patterns of genetic variation in Montezuma quail populations using nine DNA microsatellite loci. We genotyped 119 individuals from four study populations: Arizona, Western New Mexico, Central New Mexico, and West Texas. Compared to other quail, heterozygosity was low (H ¯ 0 = 0.22 ± 0.04) and there were fewer alleles per locus (Ā = 2.41 ± 0.27). The global population genetic differentiation index RST = 0.045 suggests little genetic structure, even though a Bayesian allocation analysis suggested three genetic clusters (K = 3). This analysis also suggested admixture between clusters. Nevertheless, an isolation-by-distance analysis indicates a strong correlation (r = 0.937) and moderate evidence (P = 0.032) of non-independence between geographical and genetic distances. Climate change projections indicate an increase in aridity for this region, especially in temperate ecosystems where the species occurs. In this scenario, corridors between the populations may disappear, thus causing their complete isolation.
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Affiliation(s)
| | - Alberto Macías-Duarte
- Cuerpo Académico de Recursos Naturales, Universidad Estatal de Sonora, Hermosillo, Sonora, Mexico
| | - Reyna A. Castillo-Gámez
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Alejandro Varela-Romero
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Angel B. Montoya
- Partners for Fish and Wildlife Program, United States Fish and Wildlife Service, Las Cruces, New Mexico, United States of America
| | - James H. Weaver
- Texas Parks and Wildlife Department, Fort Davis, Texas, United States of America
| | - Nohelia G. Pacheco-Hoyos
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
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7
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Lehtonen TK, Gilljam D, Veneranta L, Keskinen T, Bergenius Nord M. The ecology and fishery of the vendace (Coregonus albula) in the Baltic Sea. JOURNAL OF FISH BIOLOGY 2023; 103:1463-1475. [PMID: 37642401 DOI: 10.1111/jfb.15542] [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: 03/06/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 08/31/2023]
Abstract
Brackish water ecosystems often have high primary production, intermediate salinities, and fluctuating physical conditions and therefore provide challenging environments for many of their inhabitants. This is especially true of the Baltic Sea, which is a large body of brackish water under strong anthropogenic influence. One freshwater species that is able to cope under these conditions in the northern Baltic Sea is the vendace (Coregonus albula), a small salmonid fish. Here, we review the current knowledge of its ecology and fishery in this brackish water environment. The literature shows that, by competing for resources with other planktivores and being an important prey for a range of larger species, C. albula plays a notable role in the northern Baltic Sea ecosystem. It also sustains significant fisheries in the coastal waters of Sweden and Finland. We identify the need to better understand these C. albula populations in terms of the predator-prey interactions, distributions of anadromous and sea spawning populations and other putative (eco)morphs, extent of gene exchange between the populations, and effects of climate change on their future. In this regard, we recommend strengthening C. albula-related research and management efforts by improved collaboration and coordination between research institutions, other governmental agencies, and fishers, as well as by harmonization of fishery policies across national borders.
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Affiliation(s)
| | - David Gilljam
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Coastal Research, Öregrund, Sweden
| | | | | | - Mikaela Bergenius Nord
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research, Lysekil, Sweden
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8
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Godineau C, Fririon V, Beudez N, de Coligny F, Courbet F, Ligot G, Oddou‐Muratorio S, Sanchez L, Lefèvre F. A demo-genetic model shows how silviculture reduces natural density-dependent selection in tree populations. Evol Appl 2023; 16:1830-1844. [PMID: 38029065 PMCID: PMC10681482 DOI: 10.1111/eva.13606] [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: 03/28/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023] Open
Abstract
Biological production systems and conservation programs benefit from and should care for evolutionary processes. Developing evolution-oriented strategies requires knowledge of the evolutionary consequences of management across timescales. Here, we used an individual-based demo-genetic modelling approach to study the interactions and feedback between tree thinning, genetic evolution, and forest stand dynamics. The model combines processes that jointly drive survival and mating success-tree growth, competition and regeneration-with genetic variation of quantitative traits related to these processes. In various management and disturbance scenarios, the evolutionary rates predicted by the coupled demo-genetic model for a growth-related trait, vigor, fit within the range of empirical estimates found in the literature for wild plant and animal populations. We used this model to simulate non-selective silviculture and disturbance scenarios over four generations of trees. We characterized and quantified the effect of thinning frequencies and intensities and length of the management cycle on viability selection driven by competition and fecundity selection. The thinning regimes had a drastic long-term effect on the evolutionary rate of vigor over generations, potentially reaching 84% reduction, depending on management intensity, cycle length and disturbance regime. The reduction of genetic variance by viability selection within each generation was driven by changes in genotypic frequencies rather than by gene diversity, resulting in low-long-term erosion of the variance across generations, despite short-term fluctuations within generations. The comparison among silviculture and disturbance scenarios was qualitatively robust to assumptions on the genetic architecture of the trait. Thus, the evolutionary consequences of management result from the interference between human interventions and natural evolutionary processes. Non-selective thinning, as considered here, reduces the intensity of natural selection, while selective thinning (on tree size or other criteria) might reduce or reinforce it depending on the forester's tree choice and thinning intensity.
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Affiliation(s)
| | | | - Nicolas Beudez
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRDMontpellierFrance
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9
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Dussex N, Kurland S, Olsen RA, Spong G, Ericsson G, Ekblom R, Ryman N, Dalén L, Laikre L. Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose. Commun Biol 2023; 6:1035. [PMID: 37848497 PMCID: PMC10582009 DOI: 10.1038/s42003-023-05385-x] [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: 04/28/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.
- Norwegian University of Science and Technology, University Museum, Trondheim, NO-7491, Norway.
| | - Sara Kurland
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21, Solna, Sweden
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Göran Ericsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, SE-106 48, Stockholm, Sweden
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
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10
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Luna LW, Williams LM, Duren K, Tyl R, Toews DPL, Avery JD. Whole genome assessment of a declining game bird reveals cryptic genetic structure and insights for population management. Mol Ecol 2023; 32:5498-5513. [PMID: 37688483 DOI: 10.1111/mec.17129] [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: 03/24/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Population genomics applied to game species conservation can help delineate management units, ensure appropriate harvest levels and identify populations needing genetic rescue to safeguard their adaptive potential. The ruffed grouse (Bonasa umbellus) is rapidly declining in much of the eastern USA due to a combination of forest maturation and habitat fragmentation. More recently, mortality from West Nile Virus may have affected connectivity of local populations; however, genetic approaches have never explicitly investigated this issue. In this study, we sequenced 54 individual low-coverage (~5X) grouse genomes to characterize population structure, assess migration rates across the landscape to detect potential barriers to gene flow and identify genomic regions with high differentiation. We identified two genomic clusters with no clear geographic correlation, with large blocks of genomic differentiation associated with chromosomes 4 and 20, likely due to chromosomal inversions. After excluding these putative inversions from the data set, we found weak but nonsignificant signals of population subdivision. Estimated gene flow revealed reduced rates of migration in areas with extensive habitat fragmentation and increased genetic connectivity in areas with less habitat fragmentation. Our findings provide a benchmark for wildlife managers to compare and scale the genetic diversity and structure of ruffed grouse populations in Pennsylvania and across the eastern USA, and we also reveal structural variation in the grouse genome that requires further study to understand its possible effects on individual fitness and population distribution.
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Affiliation(s)
- Leilton W Luna
- Department of Ecosystem Science and Management, Penn State University, University Park, Pennsylvania, USA
| | - Lisa M Williams
- Bureau of Wildlife Management, Pennsylvania Game Commission, Harrisburg, Pennsylvania, USA
| | - Kenneth Duren
- Bureau of Wildlife Management, Pennsylvania Game Commission, Harrisburg, Pennsylvania, USA
| | - Reina Tyl
- Bureau of Wildlife Management, Pennsylvania Game Commission, Harrisburg, Pennsylvania, USA
| | - David P L Toews
- Department of Biology, Penn State University, University Park, Pennsylvania, USA
| | - Julian D Avery
- Department of Ecosystem Science and Management, Penn State University, University Park, Pennsylvania, USA
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11
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Ragauskas A, Ignatavičienė I, Rakauskas V, Grauda D, Prakas P, Butkauskas D. Trends of Eurasian Perch ( Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene. Animals (Basel) 2023; 13:3057. [PMID: 37835663 PMCID: PMC10571732 DOI: 10.3390/ani13193057] [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: 08/30/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability and microevolution of Perca fluviatilis within phylogeographic and anthropogenic contexts. We sequenced a 627 bp fragment encompassing the ATP6 region and used it for genetic analysis of 193 perch caught in Latvia, Lithuania, Belarus, and Ukraine, representing natural and anthropogenically impacted populations. We evaluated patterns of intraspecific genetic diversity in the ATP6 region and phylogeographic trends within the studied area compared with previously established D-loop trends. Evaluation of ATP6 coding sequence variability revealed that among 13 newly detected haplotypes, only two were caused by non-synonymous substitutions of amino acids of the protein. PCoA revealed three genetic groups (I-III) based on the ATP6 region that encompassed four previously described genetic groups established based on the mtDNA D-loop. The two mtDNA regions (D-loop and ATP6) have microevolved at least partially independently. Prolonged anthropogenic impacts may generate new point mutations at the ATP6 locus, but this phenomenon could be mainly concealed by natural selection and reparation processes.
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Affiliation(s)
- Adomas Ragauskas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Ieva Ignatavičienė
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Vytautas Rakauskas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Dace Grauda
- Institute of Biology, University of Latvia, Jelgavas Str. 1, LV-1004 Riga, Latvia;
| | - Petras Prakas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
| | - Dalius Butkauskas
- Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania; (I.I.); (V.R.); (P.P.); (D.B.)
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12
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Žunna A, Ruņģis DE, Ozoliņš J, Stepanova A, Done G. Genetic Monitoring of Grey Wolves in Latvia Shows Adverse Reproductive and Social Consequences of Hunting. BIOLOGY 2023; 12:1255. [PMID: 37759654 PMCID: PMC10525079 DOI: 10.3390/biology12091255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/17/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Nowadays, genetic research methods play an important role in animal population studies. Since 2009, genetic material from Latvian wolf specimens obtained through hunting has been systematically gathered. This study, spanning until 2021, scrutinizes the consequences of regulated wolf hunting on population genetic metrics, kinship dynamics, and social organization. We employed 16 autosomal microsatellites to investigate relationships between full siblings and parent-offspring pairs. Our analysis encompassed expected and observed heterozygosity, inbreeding coefficients, allelic diversity, genetic distance and differentiation, mean pairwise relatedness, and the number of migrants per generation. The Latvian wolf population demonstrated robust genetic diversity with minimal inbreeding, maintaining stable allelic diversity and high heterozygosity over time and it is not fragmented. Our findings reveal the persistence of conventional wolf pack structures and enduring kinship groups. However, the study also underscores the adverse effects of intensified hunting pressure, leading to breeder loss, pack disruption, territorial displacement, and the premature dispersal of juvenile wolves.
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Affiliation(s)
- Agrita Žunna
- Latvian State Forest Research Institute Silava, Rīgas Str. 111, LV-2169 Salaspils, Latvia; (D.E.R.)
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13
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Chiba S, Iwamoto A, Shimabukuro S, Matsumoto H, Inoue K. Mechanisms that can cause population decline under heavily skewed male-biased adult sex ratios. J Anim Ecol 2023; 92:1893-1903. [PMID: 37434418 DOI: 10.1111/1365-2656.13980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/13/2023]
Abstract
While adult sex ratio (ASR) is a crucial component for population management, there is still a limited understanding of how its fluctuation affects population dynamics. To demonstrate mechanisms that hinder population growth under a biased ASR, we examined changes in reproductive success with ASR using a decapod crustacean exposed to female-selective harvesting. We examined the effect of ASR on the spawning success of females. A laboratory experiment showed that the number of eggs carried by females decreased as the proportion of males in the mating groups increased. Although the same result was not observed in data collected over 25 years in the wild, the negative effect of ASR was suggested when success in carrying eggs was considered as a spawning success. These results indicate that a surplus of males results in females failing to carry eggs, probably due to sexual coercion, and the negative effect of ASR can be detected at the population level only when the bias increases because failure in spawning success occurs in part of population. We experimentally examined how male-biased sex ratios affected the maintenance of genetic diversity in a population. The diversity of paternity in a clutch increased with the number of candidate fathers. However, over 50% of a clutch was fertilised by a single male regardless of the sex ratio, and the degree of diversity was less than half of the highest diversity expected in each mating group. We also experimentally examined the mating ability of males during the breeding season. The experiment showed that multiple mating by males could not compensate for the risk that their genotypes would be lost when multiple males competed for one female. These results suggest that a male-biased ASR could trigger a decline of genetic diversity in a population. We show that ASR skewed by female-selective harvesting decreases reproductive success not only of males that have few mating opportunities but also of females. We discuss that we may still underestimate the significance of ASR on population persistence due to the difficulty of revealing the effect of ASR.
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Affiliation(s)
- Susumu Chiba
- Graduate School of Ocean and Fisheries Sciences, Tokyo University of Agriculture, Abashiri, Japan
- Department of Ocean and Fisheries Sciences, Tokyo University of Agriculture, Abashiri, Japan
| | - Aya Iwamoto
- Department of Ocean and Fisheries Sciences, Tokyo University of Agriculture, Abashiri, Japan
| | - Seina Shimabukuro
- Department of Ocean and Fisheries Sciences, Tokyo University of Agriculture, Abashiri, Japan
| | - Hiroyuki Matsumoto
- Graduate School of Ocean and Fisheries Sciences, Tokyo University of Agriculture, Abashiri, Japan
| | - Karin Inoue
- Graduate School of Ocean and Fisheries Sciences, Tokyo University of Agriculture, Abashiri, Japan
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14
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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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15
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Delord C, Petit EJ, Blanchet S, Longin G, Rinaldo R, Vigouroux R, Roussel JM, Le Bail PY, Launey S. Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value. Heredity (Edinb) 2023:10.1038/s41437-023-00616-7. [PMID: 37185615 DOI: 10.1038/s41437-023-00616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni- a major river system from the Guiana Shield -, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.
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Affiliation(s)
- Chrystelle Delord
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France.
- HYDRECO Guyane SARL, Laboratoire-Environnement de Petit Saut, 97310, Kourou, France.
- UMR MARBEC, Univ. Montpellier, IRD, Ifremer, CNRS, Sète, France.
| | - Eric J Petit
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France
| | - Simon Blanchet
- CNRS, Station d'Ecologie Théorique et Expérimentale, UAR, 2029, Moulis, France
| | | | | | - Régis Vigouroux
- HYDRECO Guyane SARL, Laboratoire-Environnement de Petit Saut, 97310, Kourou, France
| | - Jean-Marc Roussel
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France
| | | | - Sophie Launey
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 35042, Rennes, France
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16
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Kurland S, Ryman N, Hössjer O, Laikre L. Effects of subpopulation extinction on effective size (Ne) of metapopulations. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01510-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
AbstractPopulation extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.
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17
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Takagi T, Murakami R, Takano A, Torii H, Kaneko S, Tamate HB. A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer ( Cervus nippon). J Mammal 2023; 104:303-315. [PMID: 37032702 PMCID: PMC10075338 DOI: 10.1093/jmammal/gyac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/10/2022] [Indexed: 01/31/2023] Open
Abstract
Abstract
Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.
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Affiliation(s)
- Toshihito Takagi
- Fukushima University, Graduate School of Symbiotic Systems Science and Technology , Fukushima 960-1296 , Japan
| | - Ryoko Murakami
- Yamagata University, Faculty of Medicine , Yamagata 990-9585 , Japan
| | - Ayako Takano
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Harumi Torii
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Shingo Kaneko
- Fukushima University, Faculty of Symbiotic Systems Science , Fukushima 960-1296 , Japan
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18
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Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01496-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AbstractGenetic diversity is critical to a population’s ability to overcome gradual environment change. Large-bodied wildlife existing in regions with relatively high human population density are vulnerable to isolation-induced genetic drift, population bottlenecks, and loss of genetic diversity. Moose (Alces americanus americanus) in eastern North America have a complex history of drastic population changes. Current and potential threats to moose populations in this region could be exacerbated by loss of genetic diversity and connectivity among subpopulations. Existing genetic diversity, gene flow, and population clustering and fragmentation of eastern North American moose are not well quantified, while physical and anthropogenic barriers to population connectivity already exist. Here, single nucleotide polymorphism (SNP) genotyping of 507 moose spanning five northeastern U.S. states and one southeastern Canadian province indicated low diversity, with a high proportion of the genomes sharing identity-by-state, with no consistent evidence of non-random mating. Gene flow estimates indicated bidirectionality between all pairs of sampled areas, with magnitudes reflecting clustering and differentiation patterns. A Discriminant Analysis of Principal Components analysis indicated that these genotypic data were best described with four clusters and indicated connectivity across the Saint Lawrence River and Seaway, a potential physical barrier to gene flow. Tests for genetic differentiation indicated restricted gene flow between populations across the Saint Lawrence River and Seaway, and between many sampled areas facing expanding human activity. These results document current genetic variation and connectivity of moose populations in eastern North America, highlight potential challenges to current population connectivity, and identify areas for future research and conservation.
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19
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Jansson E, Faust E, Bekkevold D, Quintela M, Durif C, Halvorsen KT, Dahle G, Pampoulie C, Kennedy J, Whittaker B, Unneland L, Post S, André C, Glover KA. Global, regional, and cryptic population structure in a high gene-flow transatlantic fish. PLoS One 2023; 18:e0283351. [PMID: 36940210 PMCID: PMC10027230 DOI: 10.1371/journal.pone.0283351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, Nordnes, Bergen, Norway
| | - Ellika Faust
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Caroline Durif
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway
| | | | - Geir Dahle
- Institute of Marine Research, Nordnes, Bergen, Norway
| | | | - James Kennedy
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Benjamin Whittaker
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | | | - Søren Post
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Carl André
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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20
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Rahayu SR, Muchlisin ZA, Fadli N, Razi NM, Ramadhaniaty M, Handayani LS, Maulida S, Nur FM, Nurlaili N, Siti-Azizah MN. Morphometric and genetic variations of two dominant species of snappers (Lutjanidae) harvested from the Northern Coast of Aceh waters, Indonesia. ZOOL ANZ 2023. [DOI: 10.1016/j.jcz.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Byerly PA, Chesser RT, Fleischer RC, McInerney N, Przelomska NAS, Leberg PL. Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic. Integr Comp Biol 2022; 62:1838-1848. [PMID: 35781565 DOI: 10.1093/icb/icac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023] Open
Abstract
Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.
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Affiliation(s)
- Paige A Byerly
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - R Terry Chesser
- Eastern Ecological Science Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708, USA.,National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Nancy McInerney
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Natalia A S Przelomska
- National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA.,Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
| | - Paul L Leberg
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA
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22
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Chen RS, Soulsbury CD, Lebigre C, Ludwig G, van Oers K, Hoffman JI. Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (
Lyrurus tetrix
). Evol Appl 2022; 16:625-637. [PMID: 36969146 PMCID: PMC10033861 DOI: 10.1111/eva.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/06/2022] [Indexed: 12/28/2022] Open
Abstract
Intensive hunting activities such as commercial fishing and trophy hunting can have profound influences on natural populations. However, less intensive recreational hunting can also have subtle effects on animal behaviour, habitat use and movement, with implications for population persistence. Lekking species such as the black grouse (Lyrurus tetrix) may be especially prone to hunting as leks are temporally and spatially predictable, making them easy targets. Furthermore, inbreeding in black grouse is mainly avoided through female-biased dispersal, so any disruptions to dispersal caused by hunting could lead to changes in gene flow, increasing the risk of inbreeding. We therefore investigated the impact of hunting on genetic diversity, inbreeding and dispersal on a metapopulation of black grouse in Central Finland. We genotyped 1065 adult males and 813 adult females from twelve lekking sites (six hunted, six unhunted) and 200 unrelated chicks from seven sites (two hunted, five unhunted) at up to thirteen microsatellite loci. Our initial confirmatory analysis of sex-specific fine-scale population structure revealed little genetic structure in the metapopulation. Levels of inbreeding did not differ significantly between hunted and unhunted sites in neither adults nor chicks. However, immigration rates into hunted sites were significantly higher among adults compared to immigration into unhunted sites. We conclude that the influx of migrants into hunted sites may compensate for the loss of harvested individuals, thereby increasing gene flow and mitigating inbreeding. Given the absence of any obvious barriers to gene flow in Central Finland, a spatially heterogeneous matrix of hunted and unhunted regions may be crucial to ensure sustainable harvests into the future.
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Affiliation(s)
- Rebecca S. Chen
- Department of Animal Behaviour University of Bielefeld Bielefeld Germany
| | - Carl D. Soulsbury
- School of Life and Environmental Sciences, Joseph Banks Laboratories University of Lincoln Lincoln UK
| | - Christophe Lebigre
- UMR DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE Institut Agro Plouzané France
| | - Gilbert Ludwig
- Institute of Bioeconomy JAMK University of Applied Sciences Tarvaala Finland
| | - Kees van Oers
- Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Joseph I. Hoffman
- Department of Animal Behaviour University of Bielefeld Bielefeld Germany
- British Antarctic Survey Cambridge UK
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23
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Rohr RP, Loeuille N. Effects of evolution on niche displacement and emergent population properties, a discussion on optimality. OIKOS 2022. [DOI: 10.1111/oik.09472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rudolf P. Rohr
- 1Dept of Biology – Ecology and Evolution, Univ. of Fribourg Chemin du Musée 15 Fribourg Switzerland
| | - Nicolas Loeuille
- Sorbonne Univ., UPEC, CNRS, IRD, INRA, Inst. of Ecology and Environmental Sciences, IEES Paris France
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24
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Ausilio G, Wikenros C, Sand H, Wabakken P, Eriksen A, Zimmermann B. Environmental and anthropogenic features mediate risk from human hunters and wolves for moose. Ecosphere 2022. [DOI: 10.1002/ecs2.4323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- G. Ausilio
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
| | - C. Wikenros
- Grimsö Wildlife Research Station, Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - H. Sand
- Grimsö Wildlife Research Station, Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - P. Wabakken
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
| | - A. Eriksen
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
| | - B. Zimmermann
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
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25
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Ochoa-Zavala M, Diaz-Jaimes P, Ortega-García S, Galván-Magaña F. Genetic divergence at species boundaries of the dolphinfish ( Coryphaena hippurus) in the Tropical Eastern Pacific. PeerJ 2022; 10:e14389. [PMID: 36415864 PMCID: PMC9676019 DOI: 10.7717/peerj.14389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Marine species constitute commercially important resources, and knowledge about mechanisms that shape phylogeographic patterns and genetic structure provides valuable information for conservation. The dolphinfish, Coryphaena hippurus, is one of the most important species caught in the Tropical Eastern Pacific (TEP). However, the lack of consensus about the existence of genetically differentiated populations in the area has hindered the adoption of management strategies to ensure its viability. Methods We assessed genetic variation and phylogeographic structure using two mitochondrial genes and 14 nuclear DNA microsatellite loci. Population genetic tools were used to characterize the spatial distribution of genetic variation of C. hippurus in the TEP, evaluate the extent of connectivity between dolphinfish populations, infer potential barriers to gene flow, and test for signals of contemporary and historical demographic expansions. Results Mitochondrial DNA sequences showed genetic homogeneity across locations in the TEP, as well as a strong signal of population expansion dated to the late Pleistocene. In contrast, nuclear microsatellite markers resolved four genetically distinct groups with a remarked genetic differentiation between the most distant locations, at the northern and southern boundaries of the species' range. High mean genetic diversity was found at all localities (Hs = 0.66-0.81). Notwithstanding, positive F IS and low effective population size (Ne = 77.9-496.4) were also recorded. Conclusions The distribution of genetic variation could be related to expansion-contraction cycles following seasonal temperature changes at transitional areas, promoting population subdivisions. However, we cannot rule out the effect of oceanographic dynamics to the observed patterns. Although this marine species remains highly abundant despite commercial exploitation, the low Ne values are of conservation concern and must be considered in fishery management plans.
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Affiliation(s)
- Maried Ochoa-Zavala
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnnología, Universidad Nacional Autónoma de México, CDMX, Mexico,Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Pindaro Diaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnnología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Sofía Ortega-García
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | - Felipe Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
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Assessing Molecular Diversity in Native and Introduced Populations of Red Wood Ant Formica paralugubris. Animals (Basel) 2022; 12:ani12223165. [PMID: 36428391 PMCID: PMC9687034 DOI: 10.3390/ani12223165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
The Formica rufa group comprises several ant species which are collectively referred to as "red wood ants" and play key roles in boreal forest ecosystems, where they are ecologically dominant and greatly influence habitat dynamics. Owing to their intense predatory activity, some of these species are used as biocontrol agents against several forest insect pests and for this aim in Italy, nearly 6000 ant nests were introduced from their native areas in the Alps to several Appeninic sites during the last century. In this work, we assessed and compared the genetic variability and structure of native and introduced populations of F. paralugubris, thus evaluating the extent of genetic drift that may have occurred since the time of introduction, using amplified fragment length polymorphism (AFLP) markers. PCR amplification with a fam_EcoRI-TAC/MseI-ATG primers combination produced a total of 147 scorable bands, with 17 identified as outlier loci. The genetic variation was higher in the introduced population compared to the native ones that, on the other hand, showed a higher diversity between nests. AMOVA results clearly pointed out that the overall genetic structure was dominated by among-worker variation, considering all populations, the Alpine vs. Apennine groups and the comparison among native and related introduced populations (all ranging between 77.84% and 79.84%). Genetic analyses unveiled the existence of six main different groups that do not entirely mirror their geographic subdivision, pointing towards a wide admixture between populations, but, at the same time, rapid diversification of some Apennine populations. Future studies based on high-throughput genomic methods are needed to obtain a thorough understanding of the effects of environmental pressure on the genetic structure and mating system of these populations.
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Haye PA, Segovia NI, Vera R, Acuña E. Phylogeography reveals a panmictic population of the Chilean nylon shrimp along its exploitation range in the southeast Pacific Ocean. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Dai C. Incorporating local stakeholders' voices and knowledge into conservation decisions: a case study on the Chinese Hwamei (Garrulax canorus Linnaeus, 1758) in Taijiang, Guizhou, China. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2022; 18:63. [PMID: 36242091 PMCID: PMC9568905 DOI: 10.1186/s13002-022-00559-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The Chinese Hwamei (Garrulax canorus Linnaeus, 1758) is a widely distributed species and has long been kept as a pet, especially by the ethnic communities in Southwest China. According to conservation experts' suggestions, it has been designated as a second-level national key protected species in February, 2021 to protect this bird, indicating that keeping it at home is no longer permitted in China. However, a key factor to ensure effectiveness and success of conservation initiatives is local stakeholders' acceptance and support. METHODS Interviews and focus group discussions were used to document the policy outcomes and the views of 108 local bird-keepers in a county in Guizhou province. RESULTS Despite awareness about the illegality of the practice, the bird was still commonly caged both in rural and urban regions. To justify their unwillingness to stop keeping these birds, the interviewees presented many arguments, such as benefits for the community members' health, cultural heritage and contributions to local livelihoods. Fewer than 30% of the bird-keepers believed that the practice of self-keeping has reduced the wild population. Most argued the decline was mainly generated by the harvesting and keepers with monetary interests. They suggested enforcement should target those people and bird markets, as well as the harvesting methods. They also recommended restricting the number of birds allowed to be kept by one keeper, establishing protected areas and a harvesting ban period. The study participants demonstrated considerable local ecological knowledge about approaches for managing the species' use. CONCLUSIONS Due to the benefits for the people and the bird's large distribution, I argued that a conservation goal to lower the harvesting and keeping rates would be more appropriate than a strict ban on keeping them. Such a policy would be more feasible and culturally acceptable because it is built on keepers' support and suggestions. It is necessary to monitor the effects of bird keeping on the wild population. Overall, this qualitative study demonstrated the advantage of factoring in local voices in conservation decisions.
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Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 1 Yanzhong Road, Guilin, 541006, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, 541006, China.
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van der Reis AL, Norrie CR, Jeffs AG, Lavery SD, Carroll EL. Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster. Sci Rep 2022; 12:16783. [PMID: 36202873 PMCID: PMC9537507 DOI: 10.1038/s41598-022-19790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/05/2022] [Indexed: 11/11/2022] Open
Abstract
The emergence of high resolution population genetic techniques, such as genotyping-by-sequencing (GBS), in combination with recent advances in particle modelling of larval dispersal in marine organisms, can deliver powerful new insights to support fisheries conservation and management. In this study, we used this combination to investigate the population connectivity of a commercial deep sea lobster species, the New Zealand scampi, Metanephrops challengeri, which ranges across a vast area of seafloor around New Zealand. This species has limited dispersal capabilities, including larvae with weak swimming abilities and short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited home ranges. Ninety-one individuals, collected from five scampi fishery management areas around New Zealand, were genotyped using GBS. Using 983 haplotypic genomic loci, three genetically distinct groups were identified: eastern, southern and western. These groups showed significant genetic differentiation with clear source-sink dynamics. The direction of gene flow inferred from the genomic data largely reflected the hydrodynamic particle modelling of ocean current flow around New Zealand. The modelled dispersal during pelagic larval phase highlights the strong connectivity among eastern sampling locations and explains the low genetic differentiation detected among these sampled areas. Our results highlight the value of using a transdisciplinary approach in the inference of connectivity among populations for informing conservation and fishery management.
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Affiliation(s)
- Aimee L van der Reis
- Institute of Marine Science, University of Auckland, Auckland, New Zealand. .,School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Craig R Norrie
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, USA
| | - Andrew G Jeffs
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Shane D Lavery
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Clarke SH, McCracken GR, Humphries S, Ruzzante D, Grant JWA, Fraser DJ. Demographic resilience of brook trout populations subjected to experimental size‐selective. Evol Appl 2022; 15:1792-1805. [DOI: 10.1111/eva.13478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | - Shelley Humphries
- Lake Louise, Yoho, and Kootenay Field Unit, Parks Canada Radium Hot Springs British Columbia Canada
| | | | | | - Dylan J. Fraser
- Department of Biology Concordia University Montreal Quebec Canada
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Kilwanila SI, Lyimo CM, Rija AA. Mitochondrial genetic diversity of the Greater Cane rat (Thryonomys swinderianus) populations from the Eastern Arc Mountains ecosystem, Tanzania. Mol Biol Rep 2022; 49:10431-10442. [DOI: 10.1007/s11033-022-07823-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022]
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Grzegorczyk E, Bézier L, Le‐Rest K, Caizergues A, Francesiaz C, Champagnon J, Guillemain M, Eraud C. Is hunting nonintentionally selective? A test using game bird capture‐dead recoveries. Ecol Evol 2022; 12:e9285. [PMID: 36188522 PMCID: PMC9486496 DOI: 10.1002/ece3.9285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Selective hunting has various impacts that need to be considered for the conservation and management of harvested populations. The consequences of selective harvest have mostly been studied in trophy hunting and fishing, where selection of specific phenotypes is intentional. Recent studies, however, show that selection can also occur unintentionally. With at least 52 million birds harvested each year in Europe, it is particularly relevant to evaluate the selectivity of hunting on this taxon. Here, we considered 211,806 individuals belonging to 7 hunted bird species to study unintentional selectivity in harvest. Using linear mixed models, we compared morphological traits (mass, wing, and tarsus size) and body condition at the time of banding between birds that were subsequently recovered from hunting during the same year as their banding, and birds that were not recovered. We did not find any patterns showing systematic differences between recovery categories, among our model species, for the traits we studied. Moreover, when a difference existed between recovery categories, it was so small that its biological relevance can be challenged. Hunting of birds in Europe therefore does not show any form of strong selectivity on the morphological and physiological traits that we studied and should hence not lead to any change of these traits either by plastic or by evolutionary response.
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Affiliation(s)
- Emilienne Grzegorczyk
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Villiers‐en‐Bois France
| | - Léa Bézier
- Institut français de recherche pour l'exploitation de la mer Nantes France
| | - Kévin Le‐Rest
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Nantes France
| | - Alain Caizergues
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Nantes France
| | - Charlotte Francesiaz
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Juvignac France
| | - Jocelyn Champagnon
- Tour du Valat, Research Institute for Conservation of Mediterranean Wetlands Arles France
| | - Matthieu Guillemain
- Office Français de la Biodiversité, Conservation et Gestion Durable des Espèces Exploitées Arles France
| | - Cyril Eraud
- Office Français de la Biodiversité, Conservation et Gestion des Espèces à enjeux Villiers‐en‐Bois France
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Phukuntsi MA, Dalton DL, Mwale M, Selier J, Cebekhulu T, Sethusa MT. Genetic patterns in three South African specialist antelope species: Threats, conservation management and their implications. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Metlholo Andries Phukuntsi
- South African National Biodiversity Institute Pretoria South Africa
- Department of Environment, Water and Earth Sciences Tshwane University of Technology Pretoria South Africa
| | - Desire Lee Dalton
- South African National Biodiversity Institute Pretoria South Africa
- School of Health and Life Sciences Teesside University Middlesbrough UK
| | - Monica Mwale
- South African National Biodiversity Institute Pretoria South Africa
| | - Jeanetta Selier
- South African National Biodiversity Institute Pretoria South Africa
- School of Life Sciences University of KwaZulu‐Natal Durban South Africa
| | - Thando Cebekhulu
- South African National Biodiversity Institute Pretoria South Africa
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Using PVA and captive breeding to balance trade-offs in the rescue of the island dibbler onto a new island ark. Sci Rep 2022; 12:11913. [PMID: 35831431 PMCID: PMC9279492 DOI: 10.1038/s41598-022-14150-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/25/2022] [Indexed: 11/08/2022] Open
Abstract
In the face of the current global extinction crisis, it is critical we give conservation management strategies the best chance of success. Australia is not exempt from global trends with currently the world’s greatest mammal extinction rate (~ 1 per 8 years). Many more are threatened including the dibbler (Parantechinus apicalis) whose remnant range has been restricted to Western Australia at just one mainland site and two small offshore islands—Whitlock Island (5 ha) and Boullanger Island (35 ha). Here, we used 14 microsatellite markers to quantify genetic variation in the remaining island populations from 2013 to 2018 and incorporated these data into population viability analysis (PVA) models, used to assess factors important to dibbler survival and to provide guidance for translocations. Remnant population genetic diversity was low (< 0.3), and populations were highly divergent from each other (pairwise FSTs 0.29–0.52). Comparison of empirical data to an earlier study is consistent with recent declines in genetic diversity and models projected increasing extinction risk and declining genetic variation in the next century. Optimal translocation scenarios recommend 80 founders for new dibbler populations—provided by captive breeding—and determined the proportion of founders from parental populations to maximise genetic diversity and minimise harvesting impact. The goal of our approach is long-term survival of genetically diverse, self-sustaining populations and our methods are transferable. We consider mixing island with mainland dibblers to reinforce genetic variation.
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Genetic analysis of hog deer (Axis porcinus) in Victoria, Australia, and its applications to invasive species and game management. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01592-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractHog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland region of Victoria. Due to its status as an introduced species and an important game animal within Victoria, management of the species is complex. Given this complexity, genetic studies can provide important information regarding population structure and diversity which can assist in controlling problematic populations of hog deer, while also ensuring viable game stock in sites managed as game reserves. The aim of this study was to investigate the population genetic structure and diversity of the Victorian hog deer 150 years after introduction using short tandem repeats (STRs). Hog deer samples were collected across 15 sites of differing management regimes in the Gippsland region of Victoria and genotyped for 13 polymorphic STR loci. Up to four distinct genetic clusters were identified across the sites sampled, suggesting that despite low observed genetic diversity, population structure is present across their range. It was also possible to detect evidence of recent translocations among populations. This study suggests that the presence of distinct genetic clusters may enable management of separate genetic units, considering invasive species and game management objectives.
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Tensen L, Power J, Camacho G, Godinho R, Jansen van Vuuren B, Fischer K. Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa. Evol Appl 2022; 15:1028-1041. [PMID: 35782007 PMCID: PMC9234631 DOI: 10.1111/eva.13423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off‐take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour‐associated genes and 20 microsatellite loci in twenty Wild‐type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase‐related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human‐induced mortality rate.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences University of Koblenz‐ Landau Germany
- Department of Zoology University of Johannesburg South Africa
| | - John Power
- Directorate of Biodiversity Management, Department of Economic Development, Environment, Conservation and Tourism North West Provincial Government South Africa
| | | | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto Vairão Portugal
- Department of Zoology University of Johannesburg South Africa
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão Vairão Portugal
| | | | - Klaus Fischer
- Institute for Integrated Natural Sciences University of Koblenz‐ Landau Germany
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Scandura M, Fabbri G, Caniglia R, Iacolina L, Mattucci F, Mengoni C, Pante G, Apollonio M, Mucci N. Resilience to Historical Human Manipulations in the Genomic Variation of Italian Wild Boar Populations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.833081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human activities can globally modify natural ecosystems determining ecological, demographic and range perturbations for several animal species. These changes can jeopardize native gene pools in different ways, leading either to genetic homogenization, or conversely, to the split into genetically divergent demes. In the past decades, most European wild boar (Sus scrofa) populations were heavily managed by humans. Anthropic manipulations have strongly affected also Italian populations through heavy hunting, translocations and reintroductions that might have deeply modified their original gene pools. In this study, exploiting the availability of the well-mapped porcine genome, we applied genomic tools to explore genome-wide variability in Italian wild boar populations, investigate their genetic structure and detect signatures of possible introgression from domestic pigs and non-native wild boar. Genomic data from 134 wild boar sampled in six areas of peninsular Italy and in Sardinia were gathered using the Illumina Porcine SNP60 BeadChip (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference genotypes from European specimens and from domestic pigs (both commercial and Italian local breeds), using multivariate and maximum-likelihood approaches. Pairwise FST values, multivariate analysis and assignment procedures indicated that Italian populations were highly differentiated from all the other analyzed European wild boar populations. Overall, a lower heterozygosity was found in the Italian population than in the other European regions. The most diverging populations in Castelporziano Presidential Estate and Maremma Regional Park can be the result of long-lasting isolation, reduced population size and genetic drift. Conversely, an unexpected similarity was found among Apennine populations, even at high distances. Signatures of introgression from both non-Italian wild boar and domestic breeds were very limited. To summarize, we successfully applied genome-wide procedures to explore, for the first time, the genomic diversity of Italian wild boar, demonstrating that they represent a strongly heterogeneous assemblage of demes with different demographic and manipulation histories. Nonetheless, our results suggest that a native component of genomic variation is predominant over exogenous ones in most populations.
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Wilson KL, Bailey CJ, Davies TD, Moore JW. Marine and freshwater regime changes impact a community of migratory Pacific salmonids in decline. GLOBAL CHANGE BIOLOGY 2022; 28:72-85. [PMID: 34669231 PMCID: PMC9298309 DOI: 10.1111/gcb.15895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/31/2021] [Indexed: 05/21/2023]
Abstract
Marine and freshwater ecosystems are increasingly at risk of large and cascading changes from multiple human activities (termed "regime shifts"), which can impact population productivity, resilience, and ecosystem structure. Pacific salmon exhibit persistent and large fluctuations in their population dynamics driven by combinations of intrinsic (e.g., density dependence) and extrinsic factors (e.g., ecosystem changes, species interactions). In recent years, many Pacific salmon have declined due to regime shifts but clear understanding of the processes driving these changes remains elusive. Here, we unpacked the role of density dependence, ecosystem trends, and stochasticity on productivity regimes for a community of five anadromous Pacific salmonids (Steelhead, Coho Salmon, Pink Salmon, Dolly Varden, and Coastal Cutthroat Trout) across a rich 40-year time-series. We used a Bayesian multivariate state-space model to examine whether productivity shifts had similarly occurred across the community and explored marine or freshwater changes associated with those shifts. Overall, we identified three productivity regimes: an early regime (1976-1990), a compensatory regime (1991-2009), and a declining regime (since 2010) where large declines were observed for Steelhead, Dolly Varden, and Cutthroat Trout, intermediate declines in Coho and no change in Pink Salmon. These regime changes were associated with multiple cumulative effects across the salmon life cycle. For example, increased seal densities and ocean competition were associated with lower adult marine survival in Steelhead. Watershed logging also intensified over the past 40 years and was associated with (all else equal) ≥97% declines in freshwater productivity for Steelhead, Cutthroat, and Coho. For Steelhead, marine and freshwater dynamics played approximately equal roles in explaining trends in total productivity. Collectively, these changing environments limited juvenile production and lowered future adult returns. These results reveal how changes in freshwater and marine environments can jointly shape population dynamics among ecological communities, like Pacific salmon, with cascading consequences to their resilience.
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Affiliation(s)
- Kyle L. Wilson
- Earth to Oceans Research GroupDepartment of Biological SciencesSimon Fraser UniversityBurnabyBritish ColumbiaCanada
- Central Coast Indigenous Resource AllianceCampbell RiverBritish ColumbiaCanada
| | - Colin J. Bailey
- Earth to Oceans Research GroupDepartment of Biological SciencesSimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Trevor D. Davies
- B.C. Ministry of Forests, Lands and Natural Resource Operations and Rural Development, Fish and Aquatic Habitat BranchVictoriaBritish ColumbiaCanada
| | - Jonathan W. Moore
- Earth to Oceans Research GroupDepartment of Biological SciencesSimon Fraser UniversityBurnabyBritish ColumbiaCanada
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Honka J, Baini S, Searle JB, Kvist L, Aspi J. Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population. Ecol Evol 2022; 12:e8547. [PMID: 35127046 PMCID: PMC8796947 DOI: 10.1002/ece3.8547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-values = 0.002-0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.
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Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Serena Baini
- Department of BiologyUniversity of Rome “Tor Vergata”RomeItaly
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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Day T, Kennedy DA, Read AF, McAdams D. The economics of managing evolution. PLoS Biol 2021; 19:e3001409. [PMID: 34784349 PMCID: PMC8594813 DOI: 10.1371/journal.pbio.3001409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/07/2021] [Indexed: 11/19/2022] Open
Abstract
Humans are altering biological systems at unprecedented rates, and these alterations often have longer-term evolutionary impacts. Most obvious is the spread of resistance to pesticides and antibiotics. There are a wide variety of management strategies available to slow this evolution, and there are many reasons for using them. In this paper, we focus on the economic aspects of evolution management and ask: When is it economically beneficial for an individual decision-maker to invest in evolution management? We derive a simple dimensionless inequality showing that it is cost-effective to manage evolution when the percentage increase in the effective life span of the biological resource that management generates is larger than the percentage increase in annual profit that could be obtained by not managing evolution. We show how this inequality can be used to determine optimal investment choices for single decision-makers, to determine Nash equilibrium investment choices for multiple interacting decision-makers, and to examine how these equilibrium choices respond to regulatory interventions aimed at stimulating investment in evolution management. Our results are illustrated with examples involving Bacillus thuringiensis (Bt) crops and antibiotic use in fish farming.
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Affiliation(s)
- Troy Day
- Department of Mathematics and Statistics, Queen’s University, Kingston, Canada
- * E-mail:
| | - David A. Kennedy
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Entomology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - David McAdams
- Fuqua School of Business, Duke University, Durham, North Carolina, United States of America
- Department of Economics, Duke University, Durham, North Carolina, United States of America
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Zhao Y, Zhu X, Jiang Y, Li Z, Li X, Xu W, Wei H, Li Y, Li X. Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene. BMC Ecol Evol 2021; 21:167. [PMID: 34488635 PMCID: PMC8422745 DOI: 10.1186/s12862-021-01893-8] [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: 09/01/2020] [Accepted: 08/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding. METHODS Palaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package. RESULTS Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others. CONCLUSIONS Our study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.
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Affiliation(s)
- Yingying Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaochen Zhu
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5024, Australia
| | - Ye Jiang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhi Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Weibin Xu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hua Wei
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingdong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaodong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China. .,Panjin Guanghe Crab Industry Co. Ltd., Panjin, 124000, China.
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42
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Li W, Zhai D, Wang C, Gao X, Liu H, Cao W. Relationships Among Trophic Niche Width, Morphological Variation, and Genetic Diversity of Hemiculter leucisculus in China. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.691218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
According to the niche variation hypothesis (NVH), the populations with wider niches are phenotypically more variable than those with narrow niches. Giller expanded the NVH, suggesting that the niche width, morphological variation, and genetic diversity are all positively correlated. However, the hypothesis has been a subject of debate and discussion. In the present study, the NVH was tested by analyzing the relationships among trophic niche width, morphological variation, and genetic diversity of Hemiculter leucisculus, a widespread cyprinid fish. The fish samples were collected from six sites across Haihe, the Yellow, and the Yangtze River basins in China. The relationships among trophic niche width, morphological variation, and genetic diversity were analyzed using Pearson correlation at the inter-population level. Our analysis indicated that trophic niche width is significantly positively correlated with morphological variation, which corroborates the NVH. Morphological variation was significantly correlated to genetic diversity. However, no relationship was observed between trophic niche width and genetic diversity. We inferred that the dietary niche of H. leucisculus might change due to the plastic response toward environmental changes rather than due to the genetic variation. We also suggest that the effects of environment and heredity on the niche of the freshwater fish should be quantified separately in further studies.
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43
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Population genetics informs the management of a controversial Australian waterbird. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01393-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Pressley M, Salvioli M, Lewis DB, Richards CL, Brown JS, Staňková K. Evolutionary Dynamics of Treatment-Induced Resistance in Cancer Informs Understanding of Rapid Evolution in Natural Systems. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rapid evolution is ubiquitous in nature. We briefly review some of this quite broadly, particularly in the context of response to anthropogenic disturbances. Nowhere is this more evident, replicated and accessible to study than in cancer. Curiously cancer has been late - relative to fisheries, antibiotic resistance, pest management and evolution in human dominated landscapes - in recognizing the need for evolutionarily informed management strategies. The speed of evolution matters. Here, we employ game-theoretic modeling to compare time to progression with continuous maximum tolerable dose to that of adaptive therapy where treatment is discontinued when the population of cancer cells gets below half of its initial size and re-administered when the cancer cells recover, forming cycles with and without treatment. We show that the success of adaptive therapy relative to continuous maximum tolerable dose therapy is much higher if the population of cancer cells is defined by two cell types (sensitive vs. resistant in a polymorphic population). Additionally, the relative increase in time to progression increases with the speed of evolution. These results hold with and without a cost of resistance in cancer cells. On the other hand, treatment-induced resistance can be modeled as a quantitative trait in a monomorphic population of cancer cells. In that case, when evolution is rapid, there is no advantage to adaptive therapy. Initial responses to therapy are blunted by the cancer cells evolving too quickly. Our study emphasizes how cancer provides a unique system for studying rapid evolutionary changes within tumor ecosystems in response to human interventions; and allows us to contrast and compare this system to other human managed or dominated systems in nature.
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45
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Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters. Sci Rep 2021; 11:14874. [PMID: 34290296 PMCID: PMC8295251 DOI: 10.1038/s41598-021-94257-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
The demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.
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46
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Carroll EL, Ott PH, McMillan LF, Galletti Vernazzani B, Neveceralova P, Vermeulen E, Gaggiotti OE, Andriolo A, Baker CS, Bamford C, Best P, Cabrera E, Calderan S, Chirife A, Fewster RM, Flores PAC, Frasier T, Freitas TRO, Groch K, Hulva P, Kennedy A, Leaper R, Leslie MS, Moore M, Oliveira L, Seger J, Stepien EN, Valenzuela LO, Zerbini A, Jackson JA. Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground. J Hered 2021; 111:263-276. [PMID: 32347944 PMCID: PMC7238439 DOI: 10.1093/jhered/esaa010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/21/2020] [Indexed: 01/05/2023] Open
Abstract
As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru.
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Affiliation(s)
- Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,School of Biology, University of St Andrews, St Andrews, UK
| | - Paulo H Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Torres, RS, Brazil.,Universidade Estadual do Rio Grande do Sul, Osório, RS, Brazil
| | - Louise F McMillan
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington, New Zealand
| | | | - Petra Neveceralova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Ivanhoe Sea Safaris, Gansbaai, South Africa.,Dyer Island Conservation Trust, Great White House, Kleinbaai, Gansbaai, South Africa
| | - Els Vermeulen
- Mammal Research Institute Whale Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Artur Andriolo
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, MG, Brazil.,Instituto Aqualie, Juiz de Fora, MG, Brazil
| | - C Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Oregon State University, Newport, OR
| | - Connor Bamford
- British Antarctic Survey, Cambridge, UK.,University of Southampton, Southampton, UK
| | | | - Elsa Cabrera
- Centro de Conservación Cetacea-Casilla 19178 Correo 19, Santiago, Chile
| | | | - Andrea Chirife
- Instituto de Ciencias Biomédicas (ICB), Universidad Andrés Bello, Chile
| | - Rachel M Fewster
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Paulo A C Flores
- Área de Proteção Ambiental (Environmental Protection Area) Anhatomirim, ICMBio, MMA, Florianópolis, SC, Brazil
| | - Timothy Frasier
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Thales R O Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular- Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Karina Groch
- Instituto Australis, Imbituba, Santa Catarina, Brazil
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Amy Kennedy
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA
| | | | | | - Michael Moore
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Larissa Oliveira
- Universidade Estadual do Rio Grande do Sul, Osório, RS, Brazil.,Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, Centro de Ciências da Saúde, Sao Leopoldo, RS, Brazil
| | - Jon Seger
- School of Biological Sciences, University of Utah, Salt Lake City, UT
| | - Emilie N Stepien
- Section of Marine Mammal Research, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Luciano O Valenzuela
- School of Biological Sciences, University of Utah, Salt Lake City, UT.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Ecología Evolutiva Humana, UNCPBA, Quequén, Buenos Aires Province, Argentina.,Instituto de Conservación de Ballenas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alexandre Zerbini
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA.,Marine Ecology and Telemetry Research, Seabeck, WA.,Joint Institute for the Study of the Atmosphere and Ocean (JISAO), University of Washington, Seattle, WA
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47
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Faust E, Jansson E, André C, Halvorsen KT, Dahle G, Knutsen H, Quintela M, Glover KA. Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range. Evol Appl 2021; 14:1572-1587. [PMID: 34178105 PMCID: PMC8210792 DOI: 10.1111/eva.13220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species' distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.
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Affiliation(s)
- Ellika Faust
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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48
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Thomson AI, Archer FI, Coleman MA, Gajardo G, Goodall‐Copestake WP, Hoban S, Laikre L, Miller AD, O’Brien D, Pérez‐Espona S, Segelbacher G, Serrão EA, Sjøtun K, Stanley MS. Charting a course for genetic diversity in the UN Decade of Ocean Science. Evol Appl 2021; 14:1497-1518. [PMID: 34178100 PMCID: PMC8210796 DOI: 10.1111/eva.13224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
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Affiliation(s)
| | | | - Melinda A. Coleman
- New South Wales FisheriesNational Marine Science CentreCoffs HarbourNSWAustralia
- National Marine Science CentreSouthern Cross UniversityCoffs HarbourNSWAustralia
- Oceans Institute and School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Gonzalo Gajardo
- Laboratory of Genetics, Aquaculture & BiodiversityUniversidad de Los LagosOsornoChile
| | | | - Sean Hoban
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
| | - Linda Laikre
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
- The Wildlife Analysis UnitThe Swedish Environmental Protection AgencyStockholmSweden
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Sílvia Pérez‐Espona
- The Royal (Dick) School of Veterinary Studies and The Roslin InstituteMidlothianUK
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and ManagementUniversity FreiburgFreiburgGermany
| | - Ester A. Serrão
- CCMARCentre of Marine SciencesFaculty of Sciences and TechnologyUniversity of AlgarveFaroPortugal
| | - Kjersti Sjøtun
- Department of Biological SciencesUniversity of BergenBergenNorway
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Taboun ZS, Walter RP, Ovenden JR, Heath DD. Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure. Evol Appl 2021; 14:1286-1300. [PMID: 34025768 PMCID: PMC8127707 DOI: 10.1111/eva.13198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/01/2022] Open
Abstract
Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.
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Affiliation(s)
- Zahra S. Taboun
- Great Lakes Institute for Environmental Research (GLIER)University of WindsorWindsorOntarioCanada
| | - Ryan P. Walter
- Department of Biological ScienceCalifornia State University, FullertonFullertonCAUSA
| | - Jennifer R. Ovenden
- Molecular Fisheries LaboratorySchool of Biomedical SciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research (GLIER)University of WindsorWindsorOntarioCanada
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
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50
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Frank SC, Pelletier F, Kopatz A, Bourret A, Garant D, Swenson JE, Eiken HG, Hagen SB, Zedrosser A. Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore. Evol Appl 2021; 14:1023-1035. [PMID: 33897818 PMCID: PMC8061280 DOI: 10.1111/eva.13178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/27/2022] Open
Abstract
Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1614 brown bears, Ursus arctos, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990 to 2005, mean high: 0.28 from 2006 to 2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased, and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among "groups," even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.
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Affiliation(s)
- Shane C. Frank
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayTelemarkNorway
| | - Fanie Pelletier
- Département de BiologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Audrey Bourret
- Département de BiologieUniversité de SherbrookeSherbrookeQCCanada
| | - Dany Garant
- Département de BiologieUniversité de SherbrookeSherbrookeQCCanada
| | - Jon E. Swenson
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | | | | | - Andreas Zedrosser
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayTelemarkNorway
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Applied Life SciencesViennaAustria
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