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Onorato DP, Cunningham MW, Lotz M, Criffield M, Shindle D, Johnson A, Clemons BCF, Shea CP, Roelke-Parker ME, Johnson WE, McClintock BT, Pilgrim KL, Schwartz MK, Oli MK. Multi-generational benefits of genetic rescue. Sci Rep 2024; 14:17519. [PMID: 39080286 PMCID: PMC11289468 DOI: 10.1038/s41598-024-67033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Genetic rescue-an increase in population fitness following the introduction of new alleles-has been proven to ameliorate inbreeding depression in small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue in wildlife conservation is how long beneficial effects persist in admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers (Puma concolor coryi) across nine generations, we show that the experimental genetic rescue implemented in 1995-via the release of eight female pumas from Texas-alleviated morphological, genetic, and demographic correlates of inbreeding depression, subsequently preventing extirpation of the population. We present unequivocal evidence, for the first time in any terrestrial vertebrate, that genetic and phenotypic benefits of genetic rescue remain in this population after five generations of admixture, which helped increase panther abundance (> fivefold) and genetic effective population size (> 20-fold). Additionally, even with extensive admixture, microsatellite allele frequencies in the population continue to support the distinctness of Florida panthers from other North American puma populations, including Texas. Although threats including habitat loss, human-wildlife conflict, and infectious diseases are challenges to many imperiled populations, our results suggest genetic rescue can serve as an effective, multi-generational tool for conservation of small, isolated populations facing extinction from inbreeding.
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Affiliation(s)
- Dave P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Rd, Naples, FL, 34114, USA.
| | - Mark W Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Mark Lotz
- Division of Habitat and Species Conservation, Florida Fish and Wildlife Conservation Commission, Naples, FL, 34114, USA
| | - Marc Criffield
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Rd, Naples, FL, 34114, USA
| | - David Shindle
- US Fish and Wildlife Service, Florida Ecological Services Field Office, Immokalee, FL, 34142, USA
| | - Annette Johnson
- Big Cypress National Preserve, National Park Service, Ochopee, FL, 34141, USA
| | - Bambi C F Clemons
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Colin P Shea
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA
| | | | - Warren E Johnson
- Department of Biology, Loyola University of Maryland, Baltimore, MD, 21210, USA
| | - Brett T McClintock
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Seattle, WA, 98115, USA
| | - Kristine L Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, 59801, USA
| | - Michael K Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, 59801, USA
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA
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2
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Summers J, Cosgrove EJ, Bowman R, Fitzpatrick JW, Chen N. Impacts of increasing isolation and environmental variation on Florida Scrub-Jay demography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575127. [PMID: 38260596 PMCID: PMC10802623 DOI: 10.1101/2024.01.10.575127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively-breeding Florida Scrub-Jays ( Aphelocoma coerulescens ) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival, and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.
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3
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The Relationship between Inbreeding and Fitness Is Different between Two Genetic Lines of European Bison. DIVERSITY 2023. [DOI: 10.3390/d15030368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The pedigree data for European bison are published in the European Bison Pedigree Book, established one hundred years ago. The species passed a serious bottleneck and was kept in captivity for more than 30 years. After reintroduction, some individuals were captured and moved to enclosures, which caused gaps in pedigree data. To prevent the underestimation of inbreeding value, only animals with a fully known pedigree were used in the analysis. European bison were divided into two genetic lines, Lowland-Caucasian (LC) and Lowland (LB), with different numbers of founders (all 12 vs. 7 of them). The relation between inbreeding and survival up to one month of age, calculated using logistic regression, gave different results for every genetic line. In the LC line (N = 5441), the average inbreeding level was equal to 0.253 and the influence into survival was negative (exp(B) = 0.190), but in the LB line (N = 1227), the inbreeding level was much higher (0.410) but the influence into survival was positive (exp(B) = 6.596). It could be assumed that the difference between lines is a result of purging in the first period of species restitution.
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4
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Whiting JC, Bleich VC, Bowyer RT, Epps CW. Restoration of bighorn sheep: History, successes, and remaining conservation issues. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1083350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Mammals are imperiled worldwide, primarily from habitat loss or modification, and exhibit downward trends in their populations and distributions. Likewise, large-bodied herbivores have undergone a collapse in numbers and are at the highest extinction risk of all mammals. Bighorn sheep (Ovis canadensis) are among those large-bodied herbivores that possess a slow-paced life history, suffer from debilitating diseases, and have experienced range contractions across their historical distribution since the late 1800s. Translocations and reintroductions of these mountain ungulates are key aspects of restoration and often are used to re-establish populations in historical habitat or to supplement declining herds. Millions of US dollars and much effort by state and federal natural resource agencies, as well as public and private organizations, have been expended to restore bighorn sheep. Despite those efforts, translocated populations of bighorn sheep have not always been successful. We assessed restoration of bighorn sheep to provide insights in the context of conservation of populations of bighorn sheep, because this management tool is a frequently used to re-establish populations. We focused briefly on past efforts to restore bighorn sheep populations and followed with updates on the value of habitat enhancements, genetic issues, the importance of ecotypic or phenotypic adaptations when restoring populations, predation, and disease transmission. We also raised issues and posed questions that have potential to affect future decisions regarding the restoration of bighorn sheep. This information will help conservationists improve the success of conserving these iconic large mammals.
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5
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Ge D, Wen Z, Feijó A, Lissovsky A, Zhang W, Cheng J, Yan C, She H, Zhang D, Cheng Y, Lu L, Wu X, Mu D, Zhang Y, Xia L, Qu Y, Vogler AP, Yang Q. Genomic Consequences of and Demographic Response to Pervasive Hybridization Over Time in Climate-Sensitive Pikas. Mol Biol Evol 2022; 40:6958644. [PMID: 36562771 PMCID: PMC9847633 DOI: 10.1093/molbev/msac274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai-Tibetan Plateau (QHTP) and its vicinity have been reduced to residual populations through the movement of climatic zones during the Pleistocene and recent anthropogenic disturbance, whereas the plateau pika (O. curzoniae) remains common. Population-level whole-genome sequencing (n = 142) of six closely related species in the subgenus Ochotona revealed several phases of ancient introgression, lineage replacement, and bidirectional introgression. The strength of gene flow was the greatest from the dominant O. curzoniae to ecologically distinct species in areas peripheral to the QHTP. Genetic analyses were consistent with environmental reconstructions of past population movements. Recurrent periods of introgression throughout the Pleistocene revealed an increase in genetic variation at first but subsequent loss of genetic variation in later phases. Enhanced dispersion of introgressed genomic regions apparently contributed to demographic recovery in three peripheral species that underwent range shifts following climate oscillations on the QHTP, although it failed to drive recovery of northeastern O. dauurica and geographically isolated O. sikimaria. Our findings highlight differences in timescale and environmental background to determine the consequence of hybridization and the unique role of the QHTP in conserving key evolutionary processes of sky island species.
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Affiliation(s)
| | | | | | | | | | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinlai Wu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Danping Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yubo Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing, 100871, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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6
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Carley LN, Morris WF, Walsh R, Riebe D, Mitchell‐Olds T. Are genetic variation and demographic performance linked? Evol Appl 2022; 15:1888-1906. [PMID: 36426131 PMCID: PMC9679243 DOI: 10.1111/eva.13487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Quantifying relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. To empirically test whether and how genetic variation and population dynamics are related, we present one such paired approach. First, we use eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ S) and extinction risk of each population. We then combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, standing genetic variation and demography are weakly positively correlated. However, the inbreeding coefficient was not strongly correlated with demographic performance, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than less inbred populations. A contemporary re-census of these populations revealed that neither genetic nor demographic parameters were consistently strong predictors of current population density, although populations showing lower probabilities of extinction in demographic models had larger population sizes at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.
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Affiliation(s)
- Lauren N. Carley
- University Program in EcologyDuke UniversityDurhamNorth CarolinaUSA
- Biology DepartmentDuke UniversityDurhamNorth CarolinaUSA
- Department of Plant and Microbial BiologyUniversity of Minnesota Twin CitiesSt. PaulMinnesotaUSA
| | | | - Roberta Walsh
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Donna Riebe
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Tom Mitchell‐Olds
- Biology DepartmentDuke UniversityDurhamNorth CarolinaUSA
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
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7
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Flesch E, Graves T, Thomson J, Proffitt K, Garrott R. Average kinship within bighorn sheep populations is associated with connectivity, augmentation, and bottlenecks. Ecosphere 2022. [DOI: 10.1002/ecs2.3972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Elizabeth Flesch
- Fish and Wildlife Ecology and Management Program, Ecology Department Montana State University Bozeman Montana USA
| | - Tabitha Graves
- Glacier Field Station U.S. Geological Survey West Glacier Montana USA
| | - Jennifer Thomson
- Animal and Range Sciences Department Montana State University Bozeman Montana USA
| | | | - Robert Garrott
- Fish and Wildlife Ecology and Management Program, Ecology Department Montana State University Bozeman Montana USA
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8
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Mularo AJ, Bernal XE, DeWoody JA. Dominance can increase genetic variance after a population bottleneck: a synthesis of the theoretical and empirical evidence. J Hered 2022; 113:257-271. [PMID: 35143665 DOI: 10.1093/jhered/esac007] [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: 09/26/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on two theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.
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Affiliation(s)
- Andrew J Mularo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ximena E Bernal
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
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10
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Genetic Diversity and Divergence among Bighorn Sheep from Reintroduced Herds in Washington and Idaho. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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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: 15] [Impact Index Per Article: 5.0] [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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Multiple life-stage inbreeding depression impacts demography and extinction risk in an extinct-in-the-wild species. Sci Rep 2021; 11:682. [PMID: 33436770 PMCID: PMC7804286 DOI: 10.1038/s41598-020-79979-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Inbreeding can depress individuals’ fitness traits and reduce population viability. However, studies that directly translate inbreeding depression on fitness traits into consequences for population viability, and further, into consequences for management choices, are lacking. Here, we estimated impacts of inbreeding depression (B, lethal equivalents) across life-history stages for an extinct-in-the-wild species, the sihek (Guam kingfisher, Todiramphus cinnamominus). We then projected population growth under different management alternatives with our B estimates incorporated, as well as without inbreeding depression (B = 0) or with a conventional default B. We found that inbreeding depression severely impacted multiple life-history stages, and directly translated into an effect on population viability under management alternatives. Simulations including our B estimates indicated rapid population decline, whereas projections without inbreeding depression or with default B suggested very gradual population decline. Further, our results demonstrate that incorporation of B across life-history stages can influence management decisions, as projections with our B estimates suggested a need to switch to increased breeding management to avoid species extinction and support wild releases. Our results demonstrate that magnitude of B across life-history stages can translate into demographic consequences, such that incorporation of multiple life-stage B into population models can be important for informed conservation management decision-making.
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13
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Flesch EP, Graves TA, Thomson JM, Proffitt KM, White PJ, Stephenson TR, Garrott RA. Evaluating wildlife translocations using genomics: A bighorn sheep case study. Ecol Evol 2020; 10:13687-13704. [PMID: 33391673 PMCID: PMC7771163 DOI: 10.1002/ece3.6942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/12/2020] [Accepted: 09/25/2020] [Indexed: 01/10/2023] Open
Abstract
Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.
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Affiliation(s)
- Elizabeth P. Flesch
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
| | - Tabitha A. Graves
- Northern Rocky Mountain Science CenterU.S. Geological SurveyWest GlacierMTUSA
| | | | | | - P. J. White
- Yellowstone Center for ResourcesNational Park ServiceMammothWYUSA
| | - Thomas R. Stephenson
- Sierra Nevada Bighorn Sheep Recovery ProgramCalifornia Department of Fish and WildlifeBishopCAUSA
| | - Robert A. Garrott
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
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14
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Lowrey B, McWhirter DE, Proffitt KM, Monteith KL, Courtemanch AB, White PJ, Paterson JT, Dewey SR, Garrott RA. Individual variation creates diverse migratory portfolios in native populations of a mountain ungulate. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e2106. [PMID: 32091631 DOI: 10.1002/eap.2106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/10/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Ecological theory and empirical studies have demonstrated population-level demographic benefits resulting from a diversity of migratory behaviors with important implications for ecology, conservation, and evolution of migratory organisms. Nevertheless, evaluation of migratory portfolios (i.e., the variation in migratory behaviors across space and time among individuals within populations) has received relatively little attention in migratory ungulates, where research has focused largely on the dichotomous behaviors (e.g., resident and migrant) of partially migratory populations. Using GPS data from 361 female bighorn sheep (Ovis canadensis) across 17 (4 restored, 6 augmented, 7 native) populations in Montana and Wyoming, USA, we (1) characterized migratory portfolios based on behavioral and spatial migratory characteristics and (2) evaluated the relative influence of landscape attributes and management histories on migratory diversity. Native populations, which had been extant on the landscape for many generations, had more diverse migratory portfolios, higher behavioral switching rates, reduced seasonal range fidelity, and broad dispersion of individuals across summer and winter ranges. In contrast, restored populations with an abbreviated history on the landscape were largely non-migratory with a narrow portfolio of migratory behaviors, less behavioral switching, higher fidelity to seasonal ranges, and less dispersion on summer and winter ranges. Augmented populations were more variable and contained characteristics of both native and restored populations. Differences in migratory diversity among populations were associated with management histories (e.g., restored, augmented, or native). Landscape characteristics such as the duration and regularity of green-up, human landscape alterations, topography, and snow gradients were not strongly associated with migratory diversity. We suggest a two-pronged approach to restoring migratory portfolios in ungulates that first develops behavior-specific habitat models and then places individuals with known migratory behaviors into unoccupied areas in an effort to bolster migratory portfolios in restored populations, potentially with synergistic benefits associated with variation among individuals and resulting portfolio effects. Management efforts to restore diverse migratory portfolios may increase the abundance, resilience, and long-term viability of ungulate populations.
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Affiliation(s)
- B Lowrey
- Fish and Wildlife Ecology and Management Program, Department of Ecology, Montana State University, Bozeman, Montana, 59717, USA
| | - D E McWhirter
- Wyoming Game and Fish Department, Jackson, Wyoming, 83001, USA
| | - K M Proffitt
- Montana Department of Fish, Wildlife, and Parks, Bozeman, Montana, 59718, USA
| | - K L Monteith
- Haub School of Environment and Natural Resources, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, 82072, USA
| | - A B Courtemanch
- Wyoming Game and Fish Department, Jackson, Wyoming, 83001, USA
| | - P J White
- Yellowstone Center for Resources, Yellowstone National Park, National Park Service, Mammoth, Wyoming, 82190, USA
| | - J T Paterson
- Fish and Wildlife Ecology and Management Program, Department of Ecology, Montana State University, Bozeman, Montana, 59717, USA
| | - S R Dewey
- Grand Teton National Park, National Park Service, PO Box 170, Moose, Wyoming, 83012, USA
| | - R A Garrott
- Fish and Wildlife Ecology and Management Program, Department of Ecology, Montana State University, Bozeman, Montana, 59717, USA
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15
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Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Sci Rep 2020; 10:6582. [PMID: 32313214 PMCID: PMC7171152 DOI: 10.1038/s41598-020-63401-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/28/2020] [Indexed: 12/11/2022] Open
Abstract
Studies in laboratory animals demonstrate important relationships between environment, host traits, and microbiome composition. However, host-microbiome relationships in natural systems are understudied. Here, we investigate metapopulation-scale microbiome variation in a wild mammalian host, the desert bighorn sheep (Ovis canadensis nelsoni). We sought to identify over-represented microbial clades and understand how landscape variables and host traits influence microbiome composition across the host metapopulation. To address these questions, we performed 16S sequencing on fecal DNA samples from thirty-nine bighorn sheep across seven loosely connected populations in the Mojave Desert and assessed relationships between microbiome composition, environmental variation, geographic distribution, and microsatellite-derived host population structure and heterozygosity. We first used a phylogenetically-informed algorithm to identify bacterial clades conserved across the metapopulation. Members of genus Ruminococcaceae, genus Lachnospiraceae, and family Christensenellaceae R7 group were among the clades over-represented across the metapopulation, consistent with their known roles as rumen symbionts in domestic livestock. Additionally, compositional variation among hosts correlated with individual-level geographic and genetic structure, and with population-level differences in genetic heterozygosity. This study identifies microbiome community variation across a mammalian metapopulation, potentially associated with genetic and geographic population structure. Our results imply that microbiome composition may diverge in accordance with landscape-scale environmental and host population characteristics.
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Inbreeding reduces long-term growth of Alpine ibex populations. Nat Ecol Evol 2019; 3:1359-1364. [PMID: 31477848 DOI: 10.1038/s41559-019-0968-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/26/2019] [Indexed: 11/08/2022]
Abstract
Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species routinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial. Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly 100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in harsher environments. Populations with high average inbreeding (F ≈ 0.2) had population growth rates reduced by 71% compared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to guard against inbreeding effects in populations of endangered species have not been misplaced.
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Kerk M, Onorato DP, Hostetler JA, Bolker BM, Oli MK. Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. WILDLIFE MONOGRAPHS 2019. [DOI: 10.1002/wmon.1041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Madelon Kerk
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
| | - David P. Onorato
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 298 Sabal Palm Road Naples FL 34114 USA
| | - Jeffrey A. Hostetler
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 100 8th Avenue SE St. Petersburg FL 33701 USA
| | - Benjamin M. Bolker
- Departments of Mathematics and Statistics and Biology McMaster University 314 Hamilton Hall Hamilton ON L8S 4K1 Canada
| | - Madan K. Oli
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
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Bell DA, Robinson ZL, Funk WC, Fitzpatrick SW, Allendorf FW, Tallmon DA, Whiteley AR. The Exciting Potential and Remaining Uncertainties of Genetic Rescue. Trends Ecol Evol 2019; 34:1070-1079. [PMID: 31296345 DOI: 10.1016/j.tree.2019.06.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 02/03/2023]
Abstract
Restoring gene flow into small, isolated populations can alleviate genetic load and decrease extinction risk (i.e., genetic rescue), yet gene flow is rarely augmented as a conservation strategy. Due to this discrepancy between opportunity and action, a recent call was made for widespread genetic rescue attempts. However, several aspects of augmenting gene flow are poorly understood, including the magnitude and duration of beneficial effects and when deleterious effects are likely to occur. We discuss the remaining uncertainties of genetic rescue in order to promote and direct future research and to hasten progress toward implementing this potentially powerful conservation strategy on a broader scale.
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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
| | - W Chris Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - David A Tallmon
- Biology and Marine Biology Program, University of Alaska Southeast, Juneau, AK, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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Inbreeding depression causes reduced fecundity in Golden Retrievers. Mamm Genome 2019; 30:166-172. [PMID: 31115595 PMCID: PMC6606663 DOI: 10.1007/s00335-019-09805-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/15/2019] [Indexed: 01/09/2023]
Abstract
Inbreeding depression has been demonstrated to impact vital rates, productivity, and performance in human populations, wild and endangered species, and in recent years, the domestic species. In all cases, standardized, high-quality phenotype data on all individuals are invaluable for longitudinal analyses such as those required to evaluate vital rates of a study cohort. Further, many investigators agree upon the preference for and utility of genomic measures of inbreeding in lieu of pedigree-based estimates of inbreeding. We evaluated the association of measures of reproductive fitness in 93 Golden Retrievers enrolled in the Golden Retriever Lifetime Study with a genomic measurement of inbreeding, FROH. We demonstrate a statistically significant negative correlation between fecundity and FROH. This work sets the stage for larger scale analyses to investigate genomic regions associated with fecundity and other measures of fitness.
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20
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Gille DA, Buchalski MR, Conrad D, Rubin ES, Munig A, Wakeling BF, Epps CW, Creech TG, Crowhurst R, Holton B, Monello R, Boyce WM, Penedo MCT, Ernest HB. Genetic outcomes of translocation of bighorn sheep in Arizona. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Daphne A. Gille
- Genetics Research LaboratoryCalifornia Department of Fish and WildlifeRancho CordovaCA95670USA
- Department of Population Health and ReproductionUniversity of CaliforniaDavisCA95616USA
| | - Michael R. Buchalski
- Genetics Research LaboratoryCalifornia Department of Fish and WildlifeRancho CordovaCA95670USA
| | - Dave Conrad
- Arizona Game and Fish DepartmentPhoenixAZ85086USA
| | | | - Amber Munig
- Arizona Game and Fish DepartmentPhoenixAZ85086USA
| | | | - Clinton W. Epps
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOR97331USA
| | | | - Rachel Crowhurst
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOR97331USA
| | - Brandon Holton
- National Park ServiceGrand Canyon National ParkGrand CanyonAZ86023USA
| | - Ryan Monello
- National Park ServiceBiological Resources DivisionFort CollinsCO80525USA
| | - Walter M. Boyce
- Wildlife Health CenterUniversity of CaliforniaDavisCA95616USA
| | | | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryDepartment of Veterinary SciencesUniversity of WyomingLaramieWY82070USA
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21
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Erwin JA, Vargas K, Blais BR, Bennett K, Muldoon J, Findysz S, Christie C, Heffelfinger JR, Culver M. Genetic assessment of a bighorn sheep population expansion in the Silver Bell Mountains, Arizona. PeerJ 2018; 6:e5978. [PMID: 30533296 PMCID: PMC6276589 DOI: 10.7717/peerj.5978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 10/22/2018] [Indexed: 11/21/2022] Open
Abstract
Background The isolated population of desert bighorn sheep in the Silver Bell Mountains of southern Arizona underwent an unprecedented expansion in merely four years. We hypothesized that immigration from neighboring bighorn sheep populations could have caused the increase in numbers as detected by Arizona Game and Fish Department annual aerial counts. Methods We applied a multilocus genetic approach using mitochondrial DNA and nuclear microsatellite markers for genetic analyses to find evidence of immigration. We sampled the Silver Bell Mountains bighorn sheep before (2003) and during (2015) the population expansion, and a small number of available samples from the Gila Mountains (southwestern Arizona) and the Morenci Mine (Rocky Mountain bighorn) in an attempt to identify the source of putative immigrants and, more importantly, to serve as comparisons for genetic diversity metrics. Results We did not find evidence of substantial gene flow into the Silver Bell Mountains population. We did not detect any new mitochondrial haplotypes in the 2015 bighorn sheep samples. The microsatellite analyses detected only one new allele, in one individual from the 2015 population that was not detected in the 2003 samples. Overall, the genetic diversity of the Silver Bell Mountains population was lower than that seen in either the Gila population or the Morenci Mine population. Discussion Even though the results of this study did not help elucidate the precise reason for the recent population expansion, continued monitoring and genetic sampling could provide more clarity on the genetic demographics of this population.
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Affiliation(s)
- John A Erwin
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States of America.,James E. Rogers, College of Law, University of Arizona, Tucson, AZ, United States of America
| | - Karla Vargas
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America
| | - Brian R Blais
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America
| | - Kendell Bennett
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America
| | - Julia Muldoon
- Molecular and Cellular Biology Department, University of Arizona, Tucson, AZ, United States of America
| | - Sarah Findysz
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America
| | - Courtney Christie
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America
| | - James R Heffelfinger
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America.,Arizona Game and Fish Department, Phoenix, AZ, United States of America
| | - Melanie Culver
- US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, University of Arizona, Tucson, AZ, United States of America.,Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States of America.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States of America
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22
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Weckworth BV, Hebblewhite M, Mariani S, Musiani M. Lines on a map: conservation units, meta‐population dynamics, and recovery of woodland caribou in Canada. Ecosphere 2018. [DOI: 10.1002/ecs2.2323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Byron V. Weckworth
- Faculty of Environmental Design University of Calgary 2500 University Dr NW Calgary Alberta T2N 1N4 Canada
| | - Mark Hebblewhite
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana 32 Campus drive Missoula Montana 59812 USA
| | - Stefano Mariani
- School of Environment and Life Science University of Salford Salford M5 4WT UK
| | - Marco Musiani
- Faculty of Science, Department of Biological Sciences and Faculty of Veterinary Medicine University of Calgary 2500 University Dr NW Calgary Alberta T2N 1N4 Canada
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23
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Zhang L, Ameca y Juárez EI, Jiang Z. Viability analysis of the wild sika deer ( Cervus nippon ) population in China: Threats of habitat loss and effectiveness of management interventions. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2018.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Epps CW, Crowhurst RS, Nickerson BS. Assessing changes in functional connectivity in a desert bighorn sheep metapopulation after two generations. Mol Ecol 2018; 27:2334-2346. [PMID: 29637641 DOI: 10.1111/mec.14586] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 01/18/2023]
Abstract
Determining how species move across complex and fragmented landscapes and interact with human-made barriers is a major research focus in conservation. Studies estimating functional connectivity from movement, dispersal or gene flow usually rely on a single study period and rarely consider variation over time. We contrasted genetic structure and gene flow across barriers for a metapopulation of desert bighorn sheep (Ovis canadensis nelsoni) using genotypes collected 2000-2003 and 2013-2015. Based on the recently observed but unexpected spread of a respiratory pathogen across an interstate highway previously identified as a barrier to gene flow, we hypothesized that bighorn sheep changed how they interacted with that barrier, and that shifts in metapopulation structure influenced gene flow, genetic diversity and connectivity. Population assignment tests, genetic structure and genetic recapture demonstrated that bighorn sheep crossed the interstate highway in at least one location in 2013-2015, sharply reducing genetic structure between two populations, but supported conclusions of an earlier study that such crossings were very infrequent or unknown in 2000-2003. A recently expanded population established new links and caused decreases in genetic structure among multiple populations. Genetic diversity showed only slight increases in populations linked by new connections. Genetic structure and assignments revealed other previously undetected changes in movements and distribution, but much was consistent. Thus, we observed changes in both structural and functional connectivity over just two generations, but only in specific locations. Movement patterns of species should be revisited periodically to enable informed management, particularly in dynamic and fragmented systems.
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Affiliation(s)
- Clinton W Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon
| | - Rachel S Crowhurst
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon
| | - Brandon S Nickerson
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon
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25
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Mills LS. Some matchmaking advice when translocated immigrants are a population's last hope. Anim Conserv 2017. [DOI: 10.1111/acv.12333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Scott Mills
- Wildlife Biology Program and Office of Research and Creative Scholarship
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26
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Population Genetics and Demography Unite Ecology and Evolution. Trends Ecol Evol 2017; 32:141-152. [DOI: 10.1016/j.tree.2016.12.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/08/2016] [Accepted: 12/10/2016] [Indexed: 12/31/2022]
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Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl 2016; 9:1205-1218. [PMID: 27877200 PMCID: PMC5108213 DOI: 10.1111/eva.12414] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022] Open
Abstract
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | | | - Hans Ellegren
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gordon Luikart
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological StationDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
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Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species. Int J Genomics 2016; 2016:3460416. [PMID: 28025636 PMCID: PMC5153469 DOI: 10.1155/2016/3460416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/23/2016] [Accepted: 11/08/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.
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Buchalski MR, Sacks BN, Gille DA, Penedo MCT, Ernest HB, Morrison SA, Boyce WM. Phylogeographic and population genetic structure of bighorn sheep ( Ovis canadensis ) in North American deserts. J Mammal 2016; 97:823-838. [PMID: 29899578 PMCID: PMC5993094 DOI: 10.1093/jmammal/gyw011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Fossil data are ambiguous regarding the evolutionary origin of contemporary desert bighorn sheep ( Ovis canadensis subspecies). To address this uncertainty, we conducted phylogeographic and population genetic analyses on bighorn sheep subspecies found in southwestern North America. We analyzed 515 base pairs of mtDNA control region sequence and 39 microsatellites in 804 individuals from 58 locations. Phylogenetic analyses revealed 2 highly divergent clades concordant with Sierra Nevada ( O. c. sierrae ) and Rocky Mountain ( O. c. canadensis ) bighorn and showed that these 2 subspecies both diverged from desert bighorn prior to or during the Illinoian glaciation (~315-94 thousand years ago [kya]). Desert bighorn comprised several more recently diverged haplogroups concordant with the putative Nelson ( O. c. nelsoni ), Mexican ( O. c. mexicana ), and Peninsular ( O. c. cremnobates ) subspecies. Corresponding estimates of effective splitting times (~17-3 kya), and haplogroup ages (~85-72 kya) placed the most likely timeframe for divergence among desert bighorn subspecies somewhere within the last glacial maximum. Median-joining haplotype network and Bayesian skyline analyses both indicated that desert bighorn collectively comprised a historically large and haplotype-diverse population, which subsequently lost much of its diversity through demographic decline. Using microsatellite data, discriminant analysis of principle components (DAPC) and Bayesian clustering analyses both indicated genetic structure concordant with the geographic distribution of 3 desert subspecies. Likewise, microsatellite and mitochondrial-based FST comparisons revealed significant fixation indices among the desert bighorn genetic clusters. We conclude these desert subspecies represent ancient lineages likely descended from separate Pleistocene refugial populations and should therefore be managed as distinct taxa to preserve maximal biodiversity. Los datos de fósiles sobre el origen evolutivo de las ovejas del desierto ( Ovis canadensis subespecies) contemporáneas son ambiguos. Para dilucidar esta incertidumbre, llevamos a cabo análisis filogeográficos y de genética de poblaciones entre cinco subespecies de ovejas del suroccidente de Norteamérica. Analizamos 515 pb de secuencia de la región control del ADN mitocondrial y 39 microsatélites en 804 ovejas de 58 localidades. Los análisis filogenéticos revelaron 2 clados altamente divergentes concordantes con ovejas de la Sierra Nevada ( O. c. sierrae ) y de las Montañas Rocosas ( O. c. canadensis ), y demostraron que estas dos subespecies divergieron antes o durante la glaciación de Illinois (315,000-94,000 años). Las ovejas del desierto formaron varios haplogrupos recientemente derivados concordantes con las subespecies de Nelson ( O. c. nelsoni ), México ( O. c. mexicana ) y peninsular ( O. c. cremnobates ). Las estimaciones correspondientes al tiempo de separación efectiva (17,000-3,000 años) y edades de haplogrupos (85,000-72,000 años) son los plazos más probables para las divergencias entre subespecies de ovejas del desierto dentro de la última glaciación máxima. Análisis de redes de haplotipos de unión de medias y análisis bayesianos de líneas de horizonte indicaron que las ovejas del desierto formaron una población históricamente grande y diversa en términos de haplotipos, que luego perdieron gran parte de su diversidad a través de un descenso demográfico. Utilizando datos de microsatélites los análisis DAPC y TESS indicaron agrupamiento genético concordante con la distribución geográfica actual de las tres subespecies. Asimismo, comparaciones de FST con datos de microsatélites y mitocondriales revelaron índices de fijación significativos entre los grupos genéticos de ovejas del desierto. Concluimos que estas subespecies de ovejas del desierto representan linajes antiguos que probablemente descienden de poblaciones de distintos refugios del Pleistoceno, y que por lo tanto deben ser manejadas como taxones distintos para preservar su biodiversidad máxima.
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Miller JM, Poissant J, Malenfant RM, Hogg JT, Coltman DW. Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep. Ecol Evol 2015; 5:3401-12. [PMID: 26380673 PMCID: PMC4569035 DOI: 10.1002/ece3.1612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D', and χ ('2). We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - Jocelyn Poissant
- Centre for Ecology and Conservation, University of Exeter Penryn Campus, UK
| | - René M Malenfant
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - John T Hogg
- Montana Conservation Science Institute 5200 Upper Miller Creek Road, Missoula, Montana, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
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31
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Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015; 16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023] Open
Abstract
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1618-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - David W Coltman
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
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32
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Driscoll CC, Driscoll JG, Hazekamp C, Mitton JB, Wehausen JD. A tale of two markers: Population genetics of colorado rocky mountain bighorn sheep estimated from microsatellite and mitochondrial data. J Wildl Manage 2015. [DOI: 10.1002/jwmg.895] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Catherine C. Driscoll
- Department of Ecology and Evolutionary Biology; University of Colorado; Campus Box 224, Boulder CO 80309-0334
| | | | - Corey Hazekamp
- University of Massachusetts; 100 Morrissey Boulevard, Boston MA 02125-3393
| | - Jeffry B. Mitton
- Department of Ecology and Evolutionary Biology; University of Colorado; Campus Box 224, Boulder CO 80309-0334
| | - John D. Wehausen
- University of California San Diego; White Mountain Research Station; 3000 East Line Street, Bishop CA 93514
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Wilder BT, Betancourt JL, Epps CW, Crowhurst RS, Mead JI, Ezcurra E. Local extinction and unintentional rewilding of bighorn sheep (Ovis canadensis) on a desert island. PLoS One 2014; 9:e91358. [PMID: 24646515 PMCID: PMC3960132 DOI: 10.1371/journal.pone.0091358] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/11/2014] [Indexed: 11/18/2022] Open
Abstract
Bighorn sheep (Ovis canadensis) were not known to live on Tiburón Island, the largest island in the Gulf of California and Mexico, prior to the surprisingly successful introduction of 20 individuals as a conservation measure in 1975. Today, a stable island population of ∼500 sheep supports limited big game hunting and restocking of depleted areas on the Mexican mainland. We discovered fossil dung morphologically similar to that of bighorn sheep in a dung mat deposit from Mojet Cave, in the mountains of Tiburón Island. To determine the origin of this cave deposit we compared pellet shape to fecal pellets of other large mammals, and extracted DNA to sequence mitochondrial DNA fragments at the 12S ribosomal RNA and control regions. The fossil dung was 14C-dated to 1476-1632 calendar years before present and was confirmed as bighorn sheep by morphological and ancient DNA (aDNA) analysis. 12S sequences closely or exactly matched known bighorn sheep sequences; control region sequences exactly matched a haplotype described in desert bighorn sheep populations in southwest Arizona and southern California and showed subtle differentiation from the extant Tiburón population. Native desert bighorn sheep previously colonized this land-bridge island, most likely during the Pleistocene, when lower sea levels connected Tiburón to the mainland. They were extirpated sometime in the last ∼1500 years, probably due to inherent dynamics of isolated populations, prolonged drought, and (or) human overkill. The reintroduced population is vulnerable to similar extinction risks. The discovery presented here refutes conventional wisdom that bighorn sheep are not native to Tiburón Island, and establishes its recent introduction as an example of unintentional rewilding, defined here as the introduction of a species without knowledge that it was once native and has since gone locally extinct.
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Affiliation(s)
- Benjamin T. Wilder
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Julio L. Betancourt
- National Research Program, Water Mission Area, U.S. Geological Survey, Reston, Virginia, United States of America
| | - Clinton W. Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Rachel S. Crowhurst
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Jim I. Mead
- Department of Geosciences, and Sundquist Center of Excellence in Paleontology, East Tennessee University, Johnson City, Tennessee, United States of America
| | - Exequiel Ezcurra
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
- University of California Institute for Mexico and the United States (UC MEXUS), Riverside, California, United States of America
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Roffler GH, Talbot SL, Luikart G, Sage GK, Pilgrim KL, Adams LG, Schwartz MK. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0583-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Desert Bighorn Sheep: Changes in Genetic Variation Over Time and the Impact of Merging Populations. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2014. [DOI: 10.3996/082013-jfwm-055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Founder effects, genetic bottlenecks, and genetic drift in general can lead to low levels of genetic diversity, which can influence the persistence of populations. We examine genetic variation in two populations of desert bighorn sheep Ovis canadensis from New Mexico and Mexico to measure change over time and evaluate the impact of introducing individuals from one population into the other. Over about three generations, the amount of genetic variation in the New Mexico population increased. In contrast, over about two generations the amount of genetic variation in the Mexican population decreased by a great extent compared with an estimate from another Mexican population from which it is primarily descended. The potential reasons for these changes are discussed. In addition, although both populations have low genetic variation, introduction of Mexican rams into the New Mexico population might increase the amount of genetic variation in the New Mexico population. Overall, it appears that management to increase genetic variation might require substantial detailed monitoring and evaluation of ancestry from the different sources and fitness components.
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Olson ZH, Whittaker DG, Rhodes OE. Translocation history and genetic diversity in reintroduced bighorn sheep. J Wildl Manage 2013. [DOI: 10.1002/jwmg.624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zachary H. Olson
- Department of Forestry & Natural Resources; Purdue University; 195 Marstellar Street West Lafayette IN 47907 USA
| | - Donald G. Whittaker
- Oregon Department of Fish and Wildlife; 3406 Cherry Avenue NE Salem OR 97303 USA
| | - Olin E. Rhodes
- Department of Forestry & Natural Resources; Purdue University; 195 Marstellar Street West Lafayette IN 47907 USA
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Hedrick PW. Conservation genetics and the persistence and translocation of small populations: bighorn sheep populations as examples. Anim Conserv 2013. [DOI: 10.1111/acv.12064] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- P. W. Hedrick
- School of Life Sciences; Arizona State University; Tempe AZ USA
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Abstract
The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation. Genomic analyses can also advance management efforts for threatened wild and captive populations by identifying loci contributing to inbreeding depression and disease susceptibility, and predicting fitness consequences of introgression. However, the development of genomic tools in wild species still carries multiple challenges, particularly those associated with computational and sampling constraints. This review provides an overview of the most significant applications of NGS and the implications and limitations of genomic studies in conservation.
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Affiliation(s)
- Cynthia C Steiner
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California 92027; ; ;
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Dunham KM. Trends in populations of elephant and other large herbivores in Gonarezhou National Park, Zimbabwe, as revealed by sample aerial surveys. Afr J Ecol 2012. [DOI: 10.1111/j.1365-2028.2012.01343.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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