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Luo J, Cai Y, Xie Y, Jin X, Yu J, Xu M, Liu X, Li J. Genetic assessment of eight zoo populations of golden snub-nosed monkey ( Rhinopithecus roxellana) implication to the conservation management of captive populations. Evol Appl 2024; 17:e13726. [PMID: 38832080 PMCID: PMC11146145 DOI: 10.1111/eva.13726] [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: 09/05/2023] [Revised: 03/06/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024] Open
Abstract
Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.
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Affiliation(s)
- Jinxia Luo
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| | - Yansen Cai
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
- Department of Cell Biology and Genetic, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
| | - Yuchen Xie
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| | - Xianlin Jin
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
| | - Jianqiu Yu
- Chengdu Zoo, Chengdu Research Institute of WildlifeChengduChina
| | - Mei Xu
- Chengdu Zoo, Chengdu Research Institute of WildlifeChengduChina
| | - Xuanzhen Liu
- Chengdu Zoo, Chengdu Research Institute of WildlifeChengduChina
| | - Jing Li
- Key Laboratory of Bio‐Resources and Eco‐Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
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Dayan DI, Sard NM, Johnson MA, Fitzpatrick CK, Couture R, O'Malley KG. A single generation in the wild increases fitness for descendants of hatchery-origin Chinook salmon ( Oncorhynchus tshawytscha). Evol Appl 2024; 17:e13678. [PMID: 38617826 PMCID: PMC11009425 DOI: 10.1111/eva.13678] [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: 07/29/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/16/2024] Open
Abstract
Reintroduction is an important tool for the recovery of imperiled species. For threatened Pacific salmonids (Oncorhynchus spp.) species, hatchery-origin (HOR) individuals from a nearby source are often used to reestablish populations in vacant, historically occupied habitat. However, this approach is challenged by the relatively low reproductive success that HOR Pacific salmonids experience when they spawn in the wild, relative to their natural-origin (NOR) counterparts. In this study, we used genetic parentage analysis to compare the reproductive success of three groups of adult Chinook salmon (Oncorhynchus tshawytscha) reintroduced above Cougar Dam on the South Fork McKenzie River, Oregon: HOR Chinook salmon from an integrated stock; first-generation, wild-born descendants (hereafter F 1s) of Chinook salmon produced at the same hatchery; and NOR Chinook salmon that are presumed to have been produced below the dam, on the mainstem McKenzie River, or elsewhere and volitionally entered a trap below Cougar Dam. We found that F 1s produced nearly as many adult offspring as NORs, and 1.8-fold more adult offspring than HORs. This result suggests that, for the South Fork McKenzie reintroduction program, a single generation in the wild increases fitness for the descendants of HOR Chinook salmon. Although these results are encouraging, care must be taken before extrapolating our results to other systems.
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Affiliation(s)
- David I. Dayan
- State Fisheries Genomics Lab, Coastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation Sciences, Hatfield Marine Science CenterOregon State UniversityNewportOregonUSA
| | - Nicholas M. Sard
- Department of Biological SciencesState University of New York‐OswegoOswegoNew YorkUSA
| | - Marc A. Johnson
- Native Fish Conservation and Recovery, Oregon Department of Fish and WildlifeSalemOregonUSA
| | - Cristín K. Fitzpatrick
- State Fisheries Genomics Lab, Coastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation Sciences, Hatfield Marine Science CenterOregon State UniversityNewportOregonUSA
| | - Ryan Couture
- Oregon Department of Fish and WildlifeCorvallisOregonUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics Lab, Coastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation Sciences, Hatfield Marine Science CenterOregon State UniversityNewportOregonUSA
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Tennenbaum SR, Bortner R, Lynch C, Santymire R, Crosier A, Santiestevan J, Marinari P, Pukazhenthi BS, Comizzoli P, Hawkins MTR, Maldonado JE, Koepfli K, vonHoldt BM, DeCandia AL. Epigenetic changes to gene pathways linked to male fertility in ex situ black-footed ferrets. Evol Appl 2024; 17:e13634. [PMID: 38283602 PMCID: PMC10818088 DOI: 10.1111/eva.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
Environmental variation can influence the reproductive success of species managed under human care and in the wild, yet the mechanisms underlying this phenomenon remain largely mysterious. Molecular mechanisms such as epigenetic modifiers are important in mediating the timing and progression of reproduction in humans and model organisms, but few studies have linked epigenetic variation to reproductive fitness in wildlife. Here, we investigated epigenetic variation in black-footed ferrets (Mustela nigripes), an endangered North American mammal reliant on ex situ management for survival and persistence in the wild. Despite similar levels of genetic diversity in human-managed and wild-born populations, individuals in ex situ facilities exhibit reproductive problems, such as poor sperm quality. Differences across these settings suggest that an environmentally driven decline in reproductive capacity may be occurring in this species. We examined the role of DNA methylation, one well-studied epigenetic modifier, in this emergent condition. We leveraged blood, testes, and semen samples from male black-footed ferrets bred in ex situ facilities and found tissue-type specificity in DNA methylation across the genome, although 1360 Gene Ontology terms associated with male average litter size shared functions across tissues. We then constructed gene networks of differentially methylated genomic sites associated with three different reproductive phenotypes to explore the putative biological impact of variation in DNA methylation. Sperm gene networks associated with average litter size and sperm count were functionally enriched for candidate genes involved in reproduction, development, and its regulation through transcriptional repression. We propose that DNA methylation plays an important role in regulating these reproductive phenotypes, thereby impacting the fertility of male ex situ individuals. Our results provide information into how DNA methylation may function in the alteration of reproductive pathways and phenotypes in artificial environments. These findings provide early insights to conservation hurdles faced in the protection of this rare species.
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Affiliation(s)
| | - Robyn Bortner
- U.S. Fish & Wildlife Service National Black‐Footed Ferret Conservation CenterCarrColoradoUSA
| | | | - Rachel Santymire
- Biology DepartmentGeorgia State UniversityAtlantaGeorgiaUSA
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Adrienne Crosier
- Center for Animal Care SciencesSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Jenny Santiestevan
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Paul Marinari
- Center for Animal Care SciencesSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Budhan S. Pukazhenthi
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Pierre Comizzoli
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
| | - Melissa T. R. Hawkins
- Division of Mammals, Department of Vertebrate ZoologyNational Museum of Natural HistoryWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Klaus‐Peter Koepfli
- Center for Species SurvivalSmithsonian's National Zoo and Conservation Biology InstituteFront RoyalVirginiaUSA
- Smithsonian‐Mason School of ConservationGeorge Mason UniversityFront RoyalVirginiaUSA
| | | | - Alexandra L. DeCandia
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteWashingtonDCUSA
- BiologyGeorgetown UniversityWashingtonDCUSA
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4
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Bucholz JR, Hopper GW, González IS, Kelley TE, Jackson CR, Garrick RC, Atkinson CL, Lozier JD. Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot. Mol Ecol 2023; 32:5894-5912. [PMID: 37203688 DOI: 10.1111/mec.16991] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/16/2023] [Accepted: 05/04/2023] [Indexed: 05/20/2023]
Abstract
Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity-abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity.
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Affiliation(s)
- Jamie R Bucholz
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Garrett W Hopper
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | | | - Taylor E Kelley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Colin R Jackson
- Department of Biology, University of Mississippi, Mississippi, Mississippi, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Mississippi, Mississippi, USA
| | - Carla L Atkinson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
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5
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Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa). Genomics 2023; 115:110591. [PMID: 36849018 DOI: 10.1016/j.ygeno.2023.110591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (FIS and FROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.
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6
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Magliolo M, Naude VN, van der Merwe VC, Prost S, Orozco‐terWengel P, Burger PA, Kotze A, Grobler JP, Dalton DL. Simulated genetic efficacy of metapopulation management and conservation value of captive reintroductions in a rapidly declining felid. Anim Conserv 2022. [DOI: 10.1111/acv.12821] [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]
Affiliation(s)
- M. Magliolo
- South African National Biodiversity Institute Pretoria South Africa
- Department of Genetics University of the Free State Bloemfontein South Africa
| | - V. N. Naude
- Department of Conservation Ecology and Entomology University of Stellenbosch Matieland South Africa
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Johannesburg South Africa
| | - V. C. van der Merwe
- Endangered Wildlife Trust Johannesburg South Africa
- Institute for Communities and Wildlife in Africa University of Cape Town Cape Town South Africa
| | - S. Prost
- South African National Biodiversity Institute Pretoria South Africa
- LOEWE‐Centre for Translational Biodiversity Genomics Senckenberg Nature Research Society Frankfurt Germany
| | | | - P. A. Burger
- Department of Interdisciplinary Life Sciences Research Institute of Wildlife Ecology Vienna Austria
| | - A. Kotze
- South African National Biodiversity Institute Pretoria South Africa
- Department of Genetics University of the Free State Bloemfontein South Africa
| | - J. P. Grobler
- Department of Genetics University of the Free State Bloemfontein South Africa
| | - D. L. Dalton
- South African National Biodiversity Institute Pretoria South Africa
- School of Health and Life Sciences Teesside University Middlesbrough UK
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7
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Lamka GF, Harder AM, Sundaram M, Schwartz TS, Christie MR, DeWoody JA, Willoughby JR. Epigenetics in Ecology, Evolution, and Conservation. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.871791] [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
Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.
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8
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Yang M, Huang Y, Wu H, Li C, Ling S, Sun J, Shen H, Yue B, Zhang X. Blood transcriptome analysis revealed the immune changes and immunological adaptation of wildness training giant pandas. Mol Genet Genomics 2022; 297:227-239. [PMID: 34985592 DOI: 10.1007/s00438-021-01841-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/23/2021] [Indexed: 01/06/2023]
Abstract
The giant panda (Ailuropoda melanoleuca) is a global flagship species for biodiversity conservation. As the time for captive giant pandas to be released into the wild matures, wildness training is provided to allow adaptation to their natural environment. It is assumed that changes in the immune system would be integral in this adaptation from captive to wild, where many more pathogens would be encountered in their natural habitats. Therefore, this study aims to determine the expression changes of immune-related genes and their potential as immunoassay markers for adaptation monitoring in wildness training giant pandas, and then to understand the adaptation strategy of wildness training giant pandas to the wild environment, thereby improving the success rate of panda reintroduction. We obtained 300 differentially expressed genes (DEGs) by RNA-seq, with 239 up-regulated and 61 down-regulated DEGs in wildness training giant pandas compared to captive pandas. Functional enrichment analysis indicated that up-regulated DEGs were enriched in several immune-related terms and pathways. There were 21 immune-related DEGs, in which most of them were up-regulated in wildness training giant pandas, including several critical innate and cellular immune genes. IL1R2 was the most significantly up-regulated gene and is a signature of homeostasis within the immune system. In the protein-protein interaction (PPI) analysis, CXCL8, CXCL10, and CCL5 were identified as the hub immune genes. Our results suggested that wildness training giant pandas have stronger innate and cellular immunity than captive giant pandas, and we proposed that a gene set of CXCL8, CXCL10, CCL5, CD3D, NFKBIA, TBX21, IL12RB2, and IL1R2 may serve as potential immunoassay markers to monitor and assess the immune status of wildness training giant pandas. Our study offers the first insight into immune alterations of wildness training giant pandas, paving the way for monitoring and evaluating the immune status of giant pandas when reintroducing them into the wild.
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Affiliation(s)
- Miao Yang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Honglin Wu
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Shanshan Ling
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Jie Sun
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Haibo Shen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China.
- Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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Dolman PM, Burnside RJ, Scotland KM, Collar NJ. Captive breeding and the conservation of the threatened houbara bustards. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Translocation of captive-bred individuals to reinforce wild populations may be an important conservation approach for some species, but can be detrimental when employed to boost exploited wild populations, particularly where repeated long-term reinforcement aims to compensate for repeated unregulated offtake. We review evidence that captive breeding alters multiple physiological, life-history and temperamental traits through founder effects, genetic drift and unintended adaption to captivity; degrades learnt behaviours; and compromises biogeography, population structure and viability through introgression. We highlight these risks for the globally threatened African houbara Chlamydotis undulata and Asian houbara C. macqueenii, 2 bustard species hunted throughout much of their ranges and now subject to multiple large-scale captive-breeding programmes and translocations. In eastern Morocco, annual releases of captive-bred African houbara are 2‒3 times higher than original wild numbers, but no investigation of their potentially deleterious effects has, to our knowledge, been published, although most wild populations may now have been replaced by captive-bred domestic stock, which are reportedly not self-sustaining. Despite multiple decades of reinforcement, we are not aware of any analysis of the contribution of captive breeding to African houbara population dynamics, or of the genomic consequences. Asian houbara release programmes may also be promoting rather than preventing declines, and need to contextualise themselves through rigorous analyses of wild population numbers, demographic rates and threats, maintenance of phylogeographic concordance of released with supplemented populations, profiling of traits crucial to survival and the measurement and modelling of the impacts of reinforcement on physiological and behavioural fitness of wild populations.
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Affiliation(s)
- PM Dolman
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - RJ Burnside
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - KM Scotland
- Emirates Bird Breeding Centre for Conservation, Al Ain, Abu Dhabi, United Arab Emirates
| | - NJ Collar
- BirdLife International, Cambridge CB2 3QZ, UK
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10
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Dolman PM, Scotland KM, Burnside RJ, Collar NJ. Sustainable hunting and the conservation of the threatened houbara bustards. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Bell DA, Kovach RP, Robinson ZL, Whiteley AR, Reed TE. The ecological causes and consequences of hard and soft selection. Ecol Lett 2021; 24:1505-1521. [PMID: 33931936 DOI: 10.1111/ele.13754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 02/17/2021] [Accepted: 03/15/2021] [Indexed: 01/01/2023]
Abstract
Interactions between natural selection and population dynamics are central to both evolutionary-ecology and biological responses to anthropogenic change. Natural selection is often thought to incur a demographic cost that, at least temporarily, reduces population growth. However, hard and soft selection clarify that the influence of natural selection on population dynamics depends on ecological context. Under hard selection, an individual's fitness is independent of the population's phenotypic composition, and substantial population declines can occur when phenotypes are mismatched with the environment. In contrast, under soft selection, an individual's fitness is influenced by its phenotype relative to other interacting conspecifics. Soft selection generally influences which, but not how many, individuals survive and reproduce, resulting in little effect on population growth. Despite these important differences, the distinction between hard and soft selection is rarely considered in ecology. Here, we review and synthesize literature on hard and soft selection, explore their ecological causes and implications and highlight their conservation relevance to climate change, inbreeding depression, outbreeding depression and harvest. Overall, these concepts emphasise that natural selection and evolution may often have negligible or counterintuitive effects on population growth-underappreciated outcomes that have major implications in a rapidly changing world.
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Affiliation(s)
- Donovan A Bell
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | | | - Zachary L Robinson
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Thomas E Reed
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
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12
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Genetic interactions among native and introduced stocks of Oncorhynchus mykiss in the upper Willamette River, Oregon. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01322-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Successful Collection and Captive Rearing of Wild-Spawned Larval Klamath Suckers. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2020. [DOI: 10.3996/jfwm-20-059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Shortnose Chasmistes brevirostris and Lost River Suckers Deltistes luxatus endemic to the Klamath River Basin on the California–Oregon border have experienced dramatic population declines in parallel with many other Catostomid species. Captive propagation has become a key element of many endangered fish recovery programs, although there is little evidence of their success in restoring or recovering fish populations. We initiated a novel rearing program for Klamath suckers in 2016 with the goal of developing a husbandry strategy that better balances the ecological, genetic, and demographic risks associated with captive propagation. We collected 4,306 wild-spawned Klamath sucker larvae from a major spawning tributary May–June 2016 and reared them at a geothermal facility established through a partnership with a local landowner and aquaculture expert. Mortality during collection was <1%. We reared larvae in glass aquaria for 17–78 d until they reached approximately 30 mm total length, upon which we moved them to round fiberglass tanks for 14–46 d or until reaching approximately 60 mm total length. Overall survival of larvae to ponding for final growout was 71%. Larval tank-rearing survival was 98% for 37 d until an isolated fish health incident affected three aquarium populations, reducing survival to transfer to 75%. Survival after transfer to round fiberglass tanks for 14–46 d was 94%. This study outlines the first successful collection and early life-history husbandry of wild-spawned endangered Klamath suckers that we are aware of.
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14
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Gooley RM, Tamazian G, Castañeda‐Rico S, Murphy KR, Dobrynin P, Ferrie GM, Haefele H, Maldonado JE, Wildt DE, Pukazhenthi BS, Edwards CW, Koepfli K. Comparison of genomic diversity and structure of sable antelope ( Hippotragus niger) in zoos, conservation centers, and private ranches in North America. Evol Appl 2020; 13:2143-2154. [PMID: 32908610 PMCID: PMC7463370 DOI: 10.1111/eva.12976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/30/2022] Open
Abstract
As we enter the sixth mass extinction, many species that are no longer self-sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for holistic conservation programs between the public and private sector. Ex situ populations of sable antelope, Hippotragus niger, have existed in zoos and privately owned ranches in North America since the 1910s. Unknown founder representation and relatedness has made the genetic management of this species challenging within zoos, while populations on privately owned ranches are managed independently and retain minimal-to-no pedigree history. Consequences of such challenges include an increased risk of inbreeding and a loss of genetic diversity. Here, we developed and applied a customized targeted sequence capture panel based on 5,000 genomewide single-nucleotide polymorphisms to investigate the genomic diversity present in these uniquely managed populations. We genotyped 111 sable antelope: 23 from zoos, 43 from a single conservation center, and 45 from ranches. We found significantly higher genetic diversity and significantly lower inbreeding in herds housed in zoos and conservation centers, when compared to those in privately owned ranches, likely due to genetic-based breeding recommendations implemented in the former populations. Genetic clustering was strong among all three populations, possibly as a result of genetic drift. We propose that the North American ex situ population of sable antelope would benefit from a metapopulation management system, to halt genetic drift, reduce the occurrence of inbreeding, and enable sustainable population sizes to be managed ex situ.
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Affiliation(s)
- Rebecca M. Gooley
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome BioinformaticsSaint Petersburg State UniversitySt. PetersburgRussian Federation
| | - Susette Castañeda‐Rico
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Katherine R. Murphy
- Laboratories of Analytical BiologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
| | - Pavel Dobrynin
- Computer Technologies LaboratoryITMO UniversitySt. PetersburgRussian Federation
| | - Gina M. Ferrie
- Animals, Science and EnvironmentDisney’s Animal KingdomLake Buena VistaFLUSA
| | | | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - David E. Wildt
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Cody W. Edwards
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Department of BiologyGeorge Mason UniversityFairfaxVAUSA
| | - Klaus‐Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
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15
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van Leeuwen P, Mykytczuk N, Mastromonaco GF, Schulte‐Hostedde AI. Effects of captivity, diet, and relocation on the gut bacterial communities of white-footed mice. Ecol Evol 2020; 10:4677-4690. [PMID: 32551052 PMCID: PMC7297780 DOI: 10.1002/ece3.6221] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes can have important impacts on their host's survival. Captive breeding programs for endangered species include periods of captivity that can ultimately have an impact on reintroduction success. No study to date has investigated the impacts of captive diet on the gut microbiota during the relocation process of generalist species. This study simulated a captive breeding program with white-footed mice (Peromyscus leucopus) to describe the variability in gut microbial community structure and composition during captivity and relocation in their natural habitat, and compared it to wild individuals. Mice born in captivity were fed two different diets, a control with dry standardized pellets and a treatment with nonprocessed components that reflect a version of their wild diet that could be provided in captivity. The mice from the two groups were then relocated to their natural habitat. Relocated mice that had the treatment diet had more phylotypes in common with the wild-host microbiota than mice under the control diet or mice kept in captivity. These results have broad implications for our understanding of microbial community dynamics and the effects of captivity on reintroduced animals, including the potential impact on the survival of endangered species. This study demonstrates that ex situ conservation actions should consider a more holistic perspective of an animal's biology including its microbes.
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Affiliation(s)
- Pauline van Leeuwen
- Department of BiologyLaurentian UniversitySudburyONCanada
- Conservation Genetics LaboratoryUniversity of LiègeLiègeBelgium
| | - Nadia Mykytczuk
- Vale Living with Lakes CentreLaurentian UniversitySudburyONCanada
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16
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Pabijan M, Palomar G, Antunes B, Antoł W, Zieliński P, Babik W. Evolutionary principles guiding amphibian conservation. Evol Appl 2020; 13:857-878. [PMID: 32431739 PMCID: PMC7232768 DOI: 10.1111/eva.12940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.
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Affiliation(s)
- Maciej Pabijan
- Institute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Gemma Palomar
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bernardo Antunes
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Weronika Antoł
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Wiesław Babik
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
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17
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Lehnert SJ, Baillie SM, MacMillan J, Paterson IG, Buhariwalla CF, Bradbury IR, Bentzen P. Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout ( Salvelinus fontinalis) populations of Nova Scotia. Evol Appl 2020; 13:1069-1089. [PMID: 32431753 PMCID: PMC7232767 DOI: 10.1111/eva.12923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 12/06/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation-by-distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (<5% hatchery ancestry). Only a single location had a substantial number of hatchery-derived trout and was located in the only river where a local strain is used for supplementation. The amount of hatchery stocking within a watershed did not influence the level of hatchery introgression. Neutral genetic structure of wild populations was influenced by geography with some influence of climate and stocking indices. Overall, our study suggests that long-term stocking has not significantly affected the genetic integrity of wild trout populations, highlighting the variable outcomes of stocking and the need to evaluate the consequences on a case-by-case basis.
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Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Shauna M. Baillie
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - John MacMillan
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian G. Paterson
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Colin F. Buhariwalla
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Paul Bentzen
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
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18
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Burnside RJ, Buchan C, Salliss D, Collar NJ, Dolman PM. Releases of Asian houbara must respect genetic and geographic origin to preserve inherited migration behaviour: evidence from a translocation experiment. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200250. [PMID: 32269827 PMCID: PMC7137974 DOI: 10.1098/rsos.200250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 05/03/2023]
Abstract
Maintaining appropriate migratory strategies is important in conservation; however, translocations of migratory animals may alter locally evolved migration behaviours of recipient populations if these are different and heritable. We used satellite telemetry and experimental translocation to quantify differences and assess heritability in migration behaviours between three migratory Asian houbara (Chlamydotis macqueenii) breeding populations (640 km range across eastern, central and western Uzbekistan). Adults from the eastern population migrated twice as far (mean = 1184 km ± 44 s.e.) as the western population (656 km ± 183 s.e.) and showed significantly less variation in migration distance than the central population (1030 km ± 127 s.e.). The western and central populations wintered significantly further north (mean: +8.32° N ± 1.70 s.e. and +4.19° N ± 1.16 s.e., respectively) and the central population further west (-3.47° E ± 1.46 s.e.) than individuals from the eastern population. These differences could arise from a differing innate drive, or through learnt facultative responses to topography, filtered by survival. Translocated birds from the eastern population (wild-laid and captive-reared, n = 5) migrated further than adults from either western or central recipient populations, particularly in their second migration year. Translocated birds continued migrating south past suitable wintering grounds used by the recipient populations despite having to negotiate mountain obstacles. Together, this suggests a considerable conserved heritable migratory component with local adaptation at a fine geographic scale. Surviving translocated individuals returned to their release site, suggesting that continued translocations would lead to introgression of the heritable component and risk altering recipient migration patterns. Conservation biologists considering translocation interventions for migratory populations should evaluate potential genetic components of migratory behaviour.
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Affiliation(s)
- Robert J. Burnside
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
- Author for correspondence: Robert J. Burnside e-mail:
| | - Claire Buchan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Daniel Salliss
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Nigel J. Collar
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
- BirdLife International, Pembroke Street, Cambridge CB2 3QZ, UK
| | - Paul M. Dolman
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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19
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Derry AM, Fraser DJ, Brady SP, Astorg L, Lawrence ER, Martin GK, Matte J, Negrín Dastis JO, Paccard A, Barrett RDH, Chapman LJ, Lane JE, Ballas CG, Close M, Crispo E. Conservation through the lens of (mal)adaptation: Concepts and meta-analysis. Evol Appl 2019; 12:1287-1304. [PMID: 31417615 PMCID: PMC6691223 DOI: 10.1111/eva.12791] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/24/2019] [Accepted: 03/07/2019] [Indexed: 12/25/2022] Open
Abstract
Evolutionary approaches are gaining popularity in conservation science, with diverse strategies applied in efforts to support adaptive population outcomes. Yet conservation strategies differ in the type of adaptive outcomes they promote as conservation goals. For instance, strategies based on genetic or demographic rescue implicitly target adaptive population states whereas strategies utilizing transgenerational plasticity or evolutionary rescue implicitly target adaptive processes. These two goals are somewhat polar: adaptive state strategies optimize current population fitness, which should reduce phenotypic and/or genetic variance, reducing adaptability in changing or uncertain environments; adaptive process strategies increase genetic variance, causing maladaptation in the short term, but increase adaptability over the long term. Maladaptation refers to suboptimal population fitness, adaptation refers to optimal population fitness, and (mal)adaptation refers to the continuum of fitness variation from maladaptation to adaptation. Here, we present a conceptual classification for conservation that implicitly considers (mal)adaptation in the short-term and long-term outcomes of conservation strategies. We describe cases of how (mal)adaptation is implicated in traditional conservation strategies, as well as strategies that have potential as a conservation tool but are relatively underutilized. We use a meta-analysis of a small number of available studies to evaluate whether the different conservation strategies employed are better suited toward increasing population fitness across multiple generations. We found weakly increasing adaptation over time for transgenerational plasticity, genetic rescue, and evolutionary rescue. Demographic rescue was generally maladaptive, both immediately after conservation intervention and after several generations. Interspecific hybridization was adaptive only in the F1 generation, but then rapidly leads to maladaptation. Management decisions that are made to support the process of adaptation must adequately account for (mal)adaptation as a potential outcome and even as a tool to bolster adaptive capacity to changing conditions.
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Affiliation(s)
- Alison Margaret Derry
- Département des sciences biologiquesUniversité du Québec à MontréalMontrealQuebecCanada
- Quebec Center for Biodiversity ScienceMontrealQuebecCanada
| | - Dylan J. Fraser
- Quebec Center for Biodiversity ScienceMontrealQuebecCanada
- Biology DepartmentConcordia UniversityMontrealQuebecCanada
| | - Steven P. Brady
- Biology DepartmentSouthern Connecticut State UniversityNew HavenConnecticut
| | - Louis Astorg
- Département des sciences biologiquesUniversité du Québec à MontréalMontrealQuebecCanada
| | | | - Gillian K. Martin
- Département des sciences biologiquesUniversité du Québec à MontréalMontrealQuebecCanada
| | | | | | - Antoine Paccard
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Rowan D. H. Barrett
- Quebec Center for Biodiversity ScienceMontrealQuebecCanada
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Lauren J. Chapman
- Quebec Center for Biodiversity ScienceMontrealQuebecCanada
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Jeffrey E. Lane
- Department of BiologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | | | - Marissa Close
- Department of BiologyPace UniversityNew YorkNew York
| | - Erika Crispo
- Department of BiologyPace UniversityNew YorkNew York
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20
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Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations. Proc Natl Acad Sci U S A 2018; 116:177-186. [PMID: 30514813 DOI: 10.1073/pnas.1811559115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.
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