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Cooper RD, Shaffer HB. Managing invasive hybrids with pond hydroperiod manipulation in an endangered salamander system. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14167. [PMID: 37551773 DOI: 10.1111/cobi.14167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/07/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
When invasive and endangered native taxa hybridize, the resulting admixture introduces novel conservation challenges. Across a large region of central California, a hybrid swarm consisting of admixed endangered California tiger salamanders (CTS) (Ambystoma californiense) and introduced barred tiger salamanders (BTS) (Ambystoma mavortium) has replaced native populations, threatening the genetic integrity of CTS and the vernal pool systems they inhabit. We employed a large-scale, genomically informed field experiment to test whether shortening breeding pond hydroperiod would favor native CTS genotypes. We constructed 14 large, seminatural ponds to evaluate the effect of hydroperiod duration on larval survival and mass at metamorphosis. We tracked changes in non-native allele frequencies with a 5237-gene exon capture array and employed a combination of custom Bayesian and generalized linear models to quantify the effect of pond duration on salamander fitness. Earlier work on this system showed hybrid superiority under many conditions and suggested that hybrids are favored in human-modified ponds with artificially long hydroperiods. Consistent with these earlier studies, we found overwhelming evidence for hybrid superiority. Very short hydroperiods substantially reduced the mass (1.1-1.5 fold) and survival probability (10-13 fold) of both native and hybrid larvae, confirming that hydroperiod likely exerts a strong selective pressure in the wild. We identified 86 genes, representing 1.8% of 4723 screened loci, that significantly responded to this hydroperiod-driven selection. In contrast to earlier work, under our more natural experimental conditions, native CTS survival and size at metamorphosis were always less than hybrids, suggesting that hydroperiod management alone will not shift selection to favor native larval genotypes. However, shortening pond hydroperiod may limit productivity of hybrid ponds, complementing other strategies to remove hybrids while maintaining vernal pool ecosystems. This study confirms and expands on previous work that highlights the importance of hydroperiod management to control invasive aquatic species.
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Affiliation(s)
- Robert D Cooper
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, USA
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2
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Luttbeg B, Hammond JI, Brodin T, Sih A. Predator hunting modes and predator–prey space games. Ethology 2019. [DOI: 10.1111/eth.12998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Tomas Brodin
- Swedish University of Agricultural Sciences (SLU) Umeå Sweden
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Kovach RP, Hand BK, Hohenlohe PA, Cosart TF, Boyer MC, Neville HH, Muhlfeld CC, Amish SJ, Carim K, Narum SR, Lowe WH, Allendorf FW, Luikart G. Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones. Proc Biol Sci 2017; 283:rspb.2016.1380. [PMID: 27881749 DOI: 10.1098/rspb.2016.1380] [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: 06/17/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022] Open
Abstract
Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.
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Affiliation(s)
- Ryan P Kovach
- Northern Rocky Mountain Science Center, US Geological Survey, Missoula, MT 59802, USA
| | - Brian K Hand
- Flathead Biological Station, University of Montana, Polson, MT 59860, USA
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Ted F Cosart
- Flathead Biological Station, University of Montana, Polson, MT 59860, USA.,Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | | | | | - Clint C Muhlfeld
- Northern Rocky Mountain Science Center, US Geological Survey, Missoula, MT 59802, USA.,Flathead Biological Station, University of Montana, Polson, MT 59860, USA
| | - Stephen J Amish
- Flathead Biological Station, University of Montana, Polson, MT 59860, USA.,Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Kellie Carim
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Shawn R Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID 83332, USA
| | - Winsor H Lowe
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Fred W Allendorf
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Gordon Luikart
- Flathead Biological Station, University of Montana, Polson, MT 59860, USA.,Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, USA
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HEMATOLOGY AND PLASMA BIOCHEMISTRY INTERVALS FOR CAPTIVE-BORN CALIFORNIA TIGER SALAMANDERS (AMBYSTOMA CALIFORNIENSE). J Zoo Wildl Med 2016; 47:731-735. [DOI: 10.1638/2016-0028.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Measey GJ, Vimercati G, de Villiers FA, Mokhatla M, Davies SJ, Thorp CJ, Rebelo AD, Kumschick S. A global assessment of alien amphibian impacts in a formal framework. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12462] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- G. J. Measey
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - G. Vimercati
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - F. A. de Villiers
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - M. Mokhatla
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - S. J. Davies
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - C. J. Thorp
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - A. D. Rebelo
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
| | - S. Kumschick
- Centre for Invasion Biology; Department of Botany and Zoology; Stellenbosch University; Stellenbosch South Africa
- Invasive Species Programme; South African National Biodiversity Institute; Kirstenbosch National Botanical Gardens; Claremont 7735 South Africa
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Hwang AS, Pritchard VL, Edmands S. Recovery from hybrid breakdown in a marine invertebrate is faster, stronger and more repeatable under environmental stress. J Evol Biol 2016; 29:1793-803. [DOI: 10.1111/jeb.12913] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/30/2016] [Indexed: 11/26/2022]
Affiliation(s)
- A. S. Hwang
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - V. L. Pritchard
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - S. Edmands
- Department of Biological Sciences University of Southern California Los Angeles CA USA
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Wayne RK, Shaffer HB. Hybridization and endangered species protection in the molecular era. Mol Ecol 2016; 25:2680-9. [DOI: 10.1111/mec.13642] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/03/2016] [Accepted: 04/08/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Robert K. Wayne
- Department of Ecology and Evolutionary Biology 610 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology 610 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
- La Kretz Center for California Conservation Science Institute of the Environment and Sustainability 619 Charles E. Young Dr. South University of California Los Angeles CA 90095 USA
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Searcy CA, Shaffer HB. Do Ecological Niche Models Accurately Identify Climatic Determinants of Species Ranges? Am Nat 2016; 187:423-35. [DOI: 10.1086/685387] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
Alien herpetofauna have a broad diversity of ecological and evolutionary impacts, involving seven mechanisms. Ecological impacts usually result from trophic disruptions and may be direct or indirect and top-down or bottom-up; they may vary in scale from single species to communities. A single species may impose impacts involving most or all of these categories. Evolutionary impacts most often result from hybridization and introgression but may include diverse changes in native fauna induced by selection. Impact magnitudes observed to date largely range from moderate to major, but massive impacts (including species extinction) are known for a handful of invasive species. Research remains skewed toward a small sample of all invaders, and major research gaps remain in understanding community-level impacts, the risk posed by competition, determinants of predation impact, the relevance of genetic diversity to impacts, and how to predict impacts.
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Affiliation(s)
- Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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Shaffer HB, Gidiş M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM. Conservation genetics and genomics of amphibians and reptiles. Annu Rev Anim Biosci 2015; 3:113-38. [PMID: 25580719 DOI: 10.1146/annurev-animal-022114-110920] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.
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Wilcox JT, Padgett-Flohr GE, Alvarez JA, Johnson JR. Possible Phenotypic Influence of Superinvasive Alleles on Larval California Tiger Salamanders (Ambystoma californiense). AMERICAN MIDLAND NATURALIST 2015. [DOI: 10.1674/0003-0031-173.1.168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bucciarelli GM, Blaustein AR, Garcia TS, Kats LB. Invasion Complexities: The Diverse Impacts of Nonnative Species on Amphibians. COPEIA 2014. [DOI: 10.1643/ot-14-014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Johnson JR, Ryan ME, Micheletti SJ, Shaffer HB. Short pond hydroperiod decreases fitness of nonnative hybrid salamanders in California. Anim Conserv 2013. [DOI: 10.1111/acv.12029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- J. R. Johnson
- Department of Biology; Western Kentucky University; Bowling Green KY USA
| | - M. E. Ryan
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA USA
| | - S. J. Micheletti
- School of Biological Sciences; Washington State University; Pullman WA USA
| | - H. B. Shaffer
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
- La Kretz Center for California Conservation Science; Institute of the Environment and Sustainability; University of California; Los Angeles CA USA
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