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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [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: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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2
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Fitzpatrick SW, Mittan-Moreau C, Miller M, Judson JM. Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States. J Hered 2023; 114:354-366. [PMID: 36975379 PMCID: PMC10287150 DOI: 10.1093/jhered/esad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.
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Affiliation(s)
- Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Cinnamon Mittan-Moreau
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Madison Miller
- Savannah River Ecology Lab, University of Georgia, Aiken, SC, United States
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, United States
| | - Jessica M Judson
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
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3
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Alves F, Banks SC, Edworthy M, Stojanovic D, Langmore NE, Heinsohn R. Using conservation genetics to prioritise management options for an endangered songbird. Heredity (Edinb) 2023; 130:289-301. [PMID: 37016134 PMCID: PMC10162965 DOI: 10.1038/s41437-023-00609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.
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Affiliation(s)
- Fernanda Alves
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia.
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT, Australia
| | - Max Edworthy
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Naomi E Langmore
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
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4
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Strong bidirectional gene flow between fish lineages separated for over 100,000 years. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01476-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractRestoring levels of genetic diversity in small and declining populations is increasingly being considered in biodiversity conservation. Evidence-based genetic management requires assessment of risks and benefits of crossing populations. Because risks are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation of lineages. However, the paucity of empirical datasets on fitness consequences of longer separation times tends to favour crossing lineages with conservatively short separations, restricting wildlife managers’ options. Here, we assessed the genetic outcomes of interbreeding in the wild between lineages of a threatened Australian freshwater fish (Macquarie perch) separated by an estimated 119,000–385,000 years of evolution in distinct environments. Fish belonging to the Murray-Darling Basin (MDB) lineage escaped from Cataract Dam—into which they were translocated in ~ 1915—into the Cataract River, where they interbred with the local Hawkesbury-Nepean Basin (HNB) lineage. Analyses of reduced-representation genomic data revealed no evidence of genetic incompatibilities during interbreeding of the two lineages in the Cataract River: assignment to genotypic clusters indicated a spectrum of hybrid types including second generation hybrids and backcrosses to both parental lineages. Thus, no adverse effects were detected from genetic mixing of populations separated by > 100,000 years. We are not advocating purposely crossing the two lineages for management purposes under present cost–benefit considerations, because there are currently sufficient intra-lineage source populations to beneficially mix. Instead, this study presents a useful calibration point: two morphologically different lineages evolved in different habitats for 119,000–385,000 years can successfully interbreed.
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Klemme I, Hendrikx L, Ashrafi R, Sundberg L, Räihä V, Piironen J, Hyvärinen P, Karvonen A. Opposing health effects of hybridization for conservation. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ines Klemme
- Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland
| | - Lysanne Hendrikx
- Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland
| | - Lotta‐Riina Sundberg
- Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland
| | - Ville Räihä
- Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland
| | - Jorma Piironen
- Aquatic Population Dynamics Natural Resources Institute Paltamo Finland
| | - Pekka Hyvärinen
- Aquatic Population Dynamics Natural Resources Institute Paltamo Finland
| | - Anssi Karvonen
- Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland
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6
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Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy. Heredity (Edinb) 2021; 126:846-858. [PMID: 33608651 PMCID: PMC8102499 DOI: 10.1038/s41437-021-00413-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.
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7
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Demographic changes and loss of genetic diversity in two insular populations of bobcats (Lynx rufus). Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation. Heredity (Edinb) 2020; 125:85-100. [PMID: 32398870 DOI: 10.1038/s41437-020-0315-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 01/31/2023] Open
Abstract
Advances in sequencing technologies have revolutionized wildlife conservation genetics. Analysis of genomic data sets can provide high-resolution estimates of genetic structure, genetic diversity, gene flow, and evolutionary history. These data can be used to characterize conservation units and to effectively manage the genetic health of species in a broad evolutionary context. Here we utilize thousands of genome-wide single-nucleotide polymorphisms (SNPs) and mitochondrial DNA to provide the first genetic assessment of the Australian red-tailed black-cockatoo (Calyptorhynchus banksii), a widespread bird species comprising populations of varying conservation concern. We identified five evolutionarily significant units, which are estimated to have diverged during the Pleistocene. These units are only partially congruent with the existing morphology-based subspecies taxonomy. Genetic clusters inferred from mitochondrial DNA differed from those based on SNPs and were less resolved. Our study has a range of conservation and taxonomic implications for this species. In particular, we provide advice on the potential genetic rescue of the Endangered and restricted-range subspecies C. b. graptogyne, and propose that the western C. b. samueli population is diagnosable as a separate subspecies. The results of our study highlight the utility of considering the phylogeographic relationships inferred from genome-wide SNPs when characterizing conservation units and management priorities, which is particularly relevant as genomic data sets become increasingly accessible.
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9
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McLennan EA, Grueber CE, Wise P, Belov K, Hogg CJ. Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore. Anim Conserv 2020. [DOI: 10.1111/acv.12589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- E. A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
| | - P. Wise
- Save the Tasmanian Devil Program, DPIPWE Hobart Tas Australia
| | - K. Belov
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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10
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Genetic rescue insights from population- and family-level hybridization effects in brook trout. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01179-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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12
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Mensch EL, Kronenberger JA, Broder ED, Fitzpatrick SW, Funk WC, Angeloni LM. A potential role for immigrant reproductive behavior in the outcome of population augmentations. Anim Conserv 2019. [DOI: 10.1111/acv.12486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. L. Mensch
- Department of Biology Colorado State University Fort Collins CO USA
| | - J. A. Kronenberger
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - E. D. Broder
- Department of Biology Colorado State University Fort Collins CO USA
- Biology Department St. Ambrose University Davenport IA USA
| | - S. W. Fitzpatrick
- W.K. Kellogg Biological Station Department of Integrative Biology Michigan State University Hickory Corners MI USA
| | - W. C. Funk
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - L. M. Angeloni
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
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13
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Jahner JP, Matocq MD, Malaney JL, Cox M, Wolff P, Gritts MA, Parchman TL. The genetic legacy of 50 years of desert bighorn sheep translocations. Evol Appl 2019; 12:198-213. [PMID: 30697334 PMCID: PMC6346675 DOI: 10.1111/eva.12708] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/20/2022] Open
Abstract
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.
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Affiliation(s)
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| | - Jason L. Malaney
- Department of BiologyAustin Peay State UniversityClarksvilleTennessee
| | - Mike Cox
- Nevada Department of Wildlife, and Wild Sheep Working GroupWestern Association of Fish and Wildlife AgenciesRenoNevada
| | | | | | - Thomas L. Parchman
- Department of Biology, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
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14
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Mable BK. Conservation of adaptive potential and functional diversity: integrating old and new approaches. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1129-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Mol Ecol 2018; 27:4397-4416. [PMID: 30252986 DOI: 10.1111/mec.14877] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022]
Abstract
Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into the evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently between diverging lineages than previously thought. In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our data set. The two lineages likely diverged much more recently than previous mitochondrial estimates of 5-7 mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ~161 and 191 k generations ago. The favoured demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified gene flow among all lineages sampled. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite gene flow with surface populations. The recency of these estimated divergence events suggests that selection may drive the evolution of cave-derived traits, as opposed to disuse and drift. Finally, we show that a key trogolomorphic phenotype QTL is enriched for genomic regions with low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. Our study shows that gene flow must be considered in studies of independent, repeated trait evolution.
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Affiliation(s)
- Adam Herman
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota.,Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Yaniv Brandvain
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - James Weagley
- Ecology, Evolution, and Behavior, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Helena Bilandžija
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia.,Department of Biology, University of Maryland, College Park, Maryland
| | | | - Luis Espinasa
- School of Science, Marist College, Poughkeepsie, New York
| | - Kelly O'Quin
- Department of Biology, Centre College, Danville, Kentucky
| | - Claudia P Ornelas-García
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Masato Yoshizawa
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawaii
| | - Brian Carlson
- Department of Biology, College of Wooster, Wooster, Ohio
| | - Ernesto Maldonado
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona.,School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St Louis, Missouri
| | - Suzanne E McGaugh
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
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16
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Kronenberger JA, Gerberich JC, Fitzpatrick SW, Broder ED, Angeloni LM, Funk WC. An experimental test of alternative population augmentation scenarios. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:838-848. [PMID: 29349820 DOI: 10.1111/cobi.13076] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/19/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Human land use is fragmenting habitats worldwide and inhibiting dispersal among previously connected populations of organisms, often leading to inbreeding depression and reduced evolutionary potential in the face of rapid environmental change. To combat this augmentation of isolated populations with immigrants is sometimes used to facilitate demographic and genetic rescue. Augmentation with immigrants that are genetically and adaptively similar to the target population effectively increases population fitness, but if immigrants are very genetically or adaptively divergent, augmentation can lead to outbreeding depression. Despite well-cited guidelines for the best practice selection of immigrant sources, often only highly divergent populations remain, and experimental tests of these riskier augmentation scenarios are essentially nonexistent. We conducted a mesocosm experiment with Trinidadian guppies (Poecilia reticulata) to test the multigenerational demographic and genetic effects of augmenting 2 target populations with 3 types of divergent immigrants. We found no evidence of demographic rescue, but we did observe genetic rescue in one population. Divergent immigrant treatments tended to maintain greater genetic diversity, abundance, and hybrid fitness than controls that received immigrants from the source used to seed the mesocosms. In the second population, divergent immigrants had a slightly negative effect in one treatment, and the benefits of augmentation were less apparent overall, likely because this population started with higher genetic diversity and a lower reproductive rate that limited genetic admixture. Our results add to a growing consensus that gene flow can increase population fitness even when immigrants are more highly divergent and may help reduce uncertainty about the use of augmentation in conservation.
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Affiliation(s)
- John A Kronenberger
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523, U.S.A
- Graduate Degree Program in Ecology, Colorado State University, 1401 Campus Delivery, Fort Collins, CO, 80523, U.S.A
| | - Jill C Gerberich
- Department of Molecular Biosciences, University of Texas, NMS 3.316, STOP A5000, 2506 Speedway Austin, TX, 78712, U.S.A
| | - Sarah W Fitzpatrick
- Kellogg Biological Station, Department of Integrative Biology, Michigan State University, 3700 Gull Lake Drive E, Hickory Corners, MI, 49060, U.S.A
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, U.S.A
| | - E Dale Broder
- Interdisciplinary Research Incubator for the Study of (in)Equality, University of Denver, 2199 S University Boulevard, Denver, CO, 80208, U.S.A
| | - Lisa M Angeloni
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523, U.S.A
- Graduate Degree Program in Ecology, Colorado State University, 1401 Campus Delivery, Fort Collins, CO, 80523, U.S.A
| | - W Chris Funk
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523, U.S.A
- Graduate Degree Program in Ecology, Colorado State University, 1401 Campus Delivery, Fort Collins, CO, 80523, U.S.A
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17
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Bleich VC, Sargeant GA, Wiedmann BP. Ecotypic variation in population dynamics of reintroduced bighorn sheep. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vernon C. Bleich
- Department of Natural Resources and Environmental ScienceUniversity of Nevada Reno1664 N. Virginia Street, Mail Stop 186RenoNV89557USA
| | - Glen A. Sargeant
- U.S. Geological SurveyNorthern Prairie Wildlife Research Center8711 37th Street SEJamestownND58401USA
| | - Brett P. Wiedmann
- North Dakota Game and Fish Department225 30th Avenue SWDickinsonND58601USA
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Benazzo A, Trucchi E, Cahill JA, Maisano Delser P, Mona S, Fumagalli M, Bunnefeld L, Cornetti L, Ghirotto S, Girardi M, Ometto L, Panziera A, Rota-Stabelli O, Zanetti E, Karamanlidis A, Groff C, Paule L, Gentile L, Vilà C, Vicario S, Boitani L, Orlando L, Fuselli S, Vernesi C, Shapiro B, Ciucci P, Bertorelle G. Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers. Proc Natl Acad Sci U S A 2017; 114:E9589-E9597. [PMID: 29078308 PMCID: PMC5692547 DOI: 10.1073/pnas.1707279114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes.
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Affiliation(s)
- Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 1066, Norway
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pierpaolo Maisano Delser
- Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France
- EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France
- Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Stefano Mona
- Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France
- EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France
| | - Matteo Fumagalli
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
| | - Lynsey Bunnefeld
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Luca Cornetti
- Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Matteo Girardi
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Lino Ometto
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
- Independent Researcher, 38016 Mezzocorona, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Enrico Zanetti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Alexandros Karamanlidis
- Protection and Management of Wildlife and the Natural Environment, ARCTUROS, 53075 Aetos, Florina, Greece
| | - Claudio Groff
- Forest and Wildlife Service, Provincia Autonoma di Trento, 38100 Trento, Italy
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, 96053 Zvolen, Slovakia
| | - Leonardo Gentile
- Veterinary Service, National Park of Abruzzo Lazio and Molise, 67032 Pescasseroli, Italy
| | - Carles Vilà
- Department of Integrative Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas, 4102 Seville, Spain
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research and Technologies, National Research Council, 70126 Bari, Italy
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 K Copenhagen, Denmark
| | - Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
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Ralls K, Ballou JD, Dudash MR, Eldridge MDB, Fenster CB, Lacy RC, Sunnucks P, Frankham R. Call for a Paradigm Shift in the Genetic Management of Fragmented Populations. Conserv Lett 2017. [DOI: 10.1111/conl.12412] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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20
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Fitzpatrick SW, Handelsman CA, Torres-Dowdall J, Ruell EW, Broder ED, Kronenberger JA, Reznick DN, Ghalambor CK, Angeloni LM, Funk WC. Gene Flow Constrains and Facilitates Genetically Based Divergence in Quantitative Traits. COPEIA 2017. [DOI: 10.1643/ci-16-559] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Robinson ZL, Coombs JA, Hudy M, Nislow KH, Letcher BH, Whiteley AR. Experimental test of genetic rescue in isolated populations of brook trout. Mol Ecol 2017; 26:4418-4433. [PMID: 28664980 DOI: 10.1111/mec.14225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/21/2017] [Accepted: 06/05/2017] [Indexed: 12/27/2022]
Abstract
Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.
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Affiliation(s)
- Zachary L Robinson
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Jason A Coombs
- U.S. Forest Service, Northern Research Station, University of Massachusetts, Amherst, MA, USA
| | | | - Keith H Nislow
- U.S. Forest Service, Northern Research Station, University of Massachusetts, Amherst, MA, USA
| | - Benjamin H Letcher
- U.S. Geological Survey, Leetown Science Center, S.O. Conte Anadromous Fish Research Center, Turners Falls, MA, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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22
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Anthonysamy WJB, Dreslik MJ, Douglas MR, Thompson D, Klut GM, Kuhns AR, Mauger D, Kirk D, Glowacki GA, Douglas ME, Phillips CA. Population genetic evaluations within a co-distributed taxonomic group: a multi-species approach to conservation planning. Anim Conserv 2017. [DOI: 10.1111/acv.12365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- W. J. B. Anthonysamy
- Department of Biological Sciences; University of Arkansas; Fayetteville AR USA
- Prairie Research Institute; Illinois Natural History Survey; University of Illinois Urbana-Champaign; Champaign IL USA
| | - M. J. Dreslik
- Prairie Research Institute; Illinois Natural History Survey; University of Illinois Urbana-Champaign; Champaign IL USA
| | - M. R. Douglas
- Department of Biological Sciences; University of Arkansas; Fayetteville AR USA
| | - D. Thompson
- Forest Preserve District of DuPage County; Wheaton IL USA
| | - G. M. Klut
- Forest Preserve District of Cook County; River Forest IL USA
| | - A. R. Kuhns
- Prairie Research Institute; Illinois Natural History Survey; University of Illinois Urbana-Champaign; Champaign IL USA
| | - D. Mauger
- Forest Preserve District of Will County (Retired); Joliet IL USA
| | - D. Kirk
- Illinois Department of Natural Resources; Silver Springs State Park; Yorkville IL USA
| | | | - M. E. Douglas
- Department of Biological Sciences; University of Arkansas; Fayetteville AR USA
| | - C. A. Phillips
- Prairie Research Institute; Illinois Natural History Survey; University of Illinois Urbana-Champaign; Champaign IL USA
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23
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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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24
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Kronenberger JA, Fitzpatrick SW, Angeloni LM, Broder ED, Ruell EW, Funk WC. Playing God with guppies - informing tough conservation decisions using a model experimental system. Anim Conserv 2017. [DOI: 10.1111/acv.12341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Kronenberger
- Department of Biology; Colorado State University; Fort Collins CO USA
- Graduate Degree Program in Ecology; Colorado State University; Fort Collins CO USA
| | - S. W. Fitzpatrick
- Kellogg Biological Station; Department of Integrative Biology; Michigan State University; Hickory Corners MI USA
| | - L. M. Angeloni
- Department of Biology; Colorado State University; Fort Collins CO USA
- Graduate Degree Program in Ecology; Colorado State University; Fort Collins CO USA
| | - E. D. Broder
- Interdisciplinary Research Incubator for the Study of (in)Equality; University of Denver; Denver CO USA
| | - E. W. Ruell
- Department of Biology; Colorado State University; Fort Collins CO USA
| | - W. C. Funk
- Department of Biology; Colorado State University; Fort Collins CO USA
- Graduate Degree Program in Ecology; Colorado State University; Fort Collins CO USA
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25
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Grueber CE. Making the best of a bad situation: genetic rescue in the absence of an ideal source population. Anim Conserv 2017. [DOI: 10.1111/acv.12337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. E. Grueber
- School of Life and Environmental Sciences; Faculty of Science; The University of Sydney; NSW Australia
- San Diego Zoo Global; San Diego CA USA
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26
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