1
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Dayan DI, Sard NM, Johnson MA, Fitzpatrick CK, Couture R, O'Malley KG. A single generation in the wild increases fitness for descendants of hatchery-origin Chinook salmon ( Oncorhynchus tshawytscha). Evol Appl 2024; 17:e13678. [PMID: 38617826 PMCID: PMC11009425 DOI: 10.1111/eva.13678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/16/2024] Open
Abstract
Reintroduction is an important tool for the recovery of imperiled species. For threatened Pacific salmonids (Oncorhynchus spp.) species, hatchery-origin (HOR) individuals from a nearby source are often used to reestablish populations in vacant, historically occupied habitat. However, this approach is challenged by the relatively low reproductive success that HOR Pacific salmonids experience when they spawn in the wild, relative to their natural-origin (NOR) counterparts. In this study, we used genetic parentage analysis to compare the reproductive success of three groups of adult Chinook salmon (Oncorhynchus tshawytscha) reintroduced above Cougar Dam on the South Fork McKenzie River, Oregon: HOR Chinook salmon from an integrated stock; first-generation, wild-born descendants (hereafter F 1s) of Chinook salmon produced at the same hatchery; and NOR Chinook salmon that are presumed to have been produced below the dam, on the mainstem McKenzie River, or elsewhere and volitionally entered a trap below Cougar Dam. We found that F 1s produced nearly as many adult offspring as NORs, and 1.8-fold more adult offspring than HORs. This result suggests that, for the South Fork McKenzie reintroduction program, a single generation in the wild increases fitness for the descendants of HOR Chinook salmon. Although these results are encouraging, care must be taken before extrapolating our results to other systems.
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Affiliation(s)
- David I. Dayan
- State Fisheries Genomics Lab, Coastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation Sciences, Hatfield Marine Science CenterOregon State UniversityNewportOregonUSA
| | - Nicholas M. Sard
- Department of Biological SciencesState University of New York‐OswegoOswegoNew YorkUSA
| | - Marc A. Johnson
- Native Fish Conservation and Recovery, Oregon Department of Fish and WildlifeSalemOregonUSA
| | - Cristín K. Fitzpatrick
- State Fisheries Genomics Lab, Coastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation Sciences, Hatfield Marine Science CenterOregon State UniversityNewportOregonUSA
| | - Ryan Couture
- Oregon Department of Fish and WildlifeCorvallisOregonUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics Lab, Coastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation Sciences, Hatfield Marine Science CenterOregon State UniversityNewportOregonUSA
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2
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Reid JM, Dickel L, Keller LF, Nietlisbach P, Arcese P. Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population. Ecol Lett 2024; 27:e14377. [PMID: 38361472 DOI: 10.1111/ele.14377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/17/2024]
Abstract
Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. However, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, altering multiple eco-evolutionary implications of immigration.
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Affiliation(s)
- Jane M Reid
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Lisa Dickel
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Natural History Museum, University of Zurich, Zurich, Switzerland
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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3
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May SA, Shedd KR, Rand PS, Westley PAH. Tidal gradients, fine-scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha). Mol Ecol 2023; 32:5838-5848. [PMID: 37830261 DOI: 10.1111/mec.17154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site-choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine-scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound.
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Affiliation(s)
- Samuel A May
- Department of Fisheries, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Kyle R Shedd
- Alaska Department of Fish & Game, Anchorage, Alaska, USA
| | - Peter S Rand
- Prince William Sound Science Center (PWSSC), Cordova, Alaska, USA
| | - Peter A H Westley
- Department of Fisheries, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
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4
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Euclide PT, Larson WA, Shi Y, Gruenthal K, Christensen KA, Seeb J, Seeb L. Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms. Mol Ecol 2023. [PMID: 37695544 DOI: 10.1111/mec.17126] [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: 05/09/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
Local adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. The mechanisms that create and maintain these islands and how they contribute to adaptive divergence is an active research topic. Here, we use sockeye salmon as a model to investigate both the mechanisms responsible for creating islands of divergence and the patterns of differentiation at these islands. Previous research suggested that multiple islands contributed to adaptive radiation of sockeye salmon. However, the low-density genomic methods used by these studies made it difficult to fully elucidate the mechanisms responsible for islands and connect genotypes to adaptive variation. We used whole genome resequencing to genotype millions of loci to investigate patterns of genetic variation at islands and the mechanisms that potentially created them. We discovered 64 islands, including 16 clustered in four genomic regions shared between two isolated populations. Characterisation of these four regions suggested that three were likely created by structural variation, while one was created by processes not involving structural variation. All four regions were small (< 600 kb), suggesting low recombination regions do not have to span megabases to be important for adaptive divergence. Differentiation at islands was not consistently associated with established population attributes. In sum, the landscape of adaptive divergence and the mechanisms that create it are complex; this complexity likely helps to facilitate fine-scale local adaptation unique to each population.
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Affiliation(s)
- Peter T Euclide
- Department of Forestry and Natural Resources, Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, Juneau, Alaska, USA
| | - Yue Shi
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Kristen Gruenthal
- Alaska Department of Fish and Game, Juneau, Alaska, USA
- Office of Applied Science, Wisconsin Department of Natural Resources, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Jim Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Lisa Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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5
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Dressler TL, Han Lee V, Klose K, Eliason EJ. Thermal tolerance and vulnerability to warming differ between populations of wild Oncorhynchus mykiss near the species' southern range limit. Sci Rep 2023; 13:14538. [PMID: 37666931 PMCID: PMC10477306 DOI: 10.1038/s41598-023-41173-7] [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: 02/15/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023] Open
Abstract
Fish habitat temperatures are increasing due to human impacts including climate change. For broadly distributed species, thermal tolerance can vary at the population level, making it challenging to predict which populations are most vulnerable to warming. Populations inhabiting warm range boundaries may be more resilient to these changes due to adaptation or acclimatization to warmer temperatures, or they may be more vulnerable as temperatures may already approach their physiological limits. We tested functional and critical thermal tolerance of two populations of wild Oncorhynchus mykiss near the species' southern range limit and, as predicted, found population-specific responses to temperature. Specifically, the population inhabiting the warmer stream, Piru Creek, had higher critical thermal maxima and higher functional thermal tolerance compared to the population from the cooler stream, Arroyo Seco. Arroyo Seco O. mykiss are more likely to experience a limitation of aerobic scope with warming. Piru Creek O. mykiss, however, had higher resting metabolic rates and prolonged exercise recovery, meaning that they could be more vulnerable to warming if prey or dissolved oxygen become limited. Temperature varies widely between streams near the O. mykiss southern range limit and populations will likely have unique responses to warming based on their thermal tolerances and metabolic requirements.
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Affiliation(s)
- T L Dressler
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - V Han Lee
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - K Klose
- U.S. Forest Service, Los Padres National Forest, 1980 Old Mission Drive, Solvang, CA, 93463, USA
| | - E J Eliason
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106, USA.
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6
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Conservation genomics reveals low connectivity among populations of threatened roseate terns (Sterna dougallii) in the Atlantic Basin. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01505-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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7
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May SA, Hard JJ, Ford MJ, Naish KA, Ward EJ. Assortative mating for reproductive timing affects population recruitment and resilience in a quantitative genetic model. Evol Appl 2023; 16:657-672. [PMID: 36969143 PMCID: PMC10033844 DOI: 10.1111/eva.13524] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/12/2022] [Indexed: 01/22/2023] Open
Abstract
Quantitative models that simulate the inheritance and evolution of fitness-linked traits offer a method for predicting how environmental or anthropogenic perturbations can affect the dynamics of wild populations. Random mating between individuals within populations is a key assumption of many such models used in conservation and management to predict the impacts of proposed management or conservation actions. However, recent evidence suggests that non-random mating may be underestimated in wild populations and play an important role in diversity-stability relationships. Here we introduce a novel individual-based quantitative genetic model that incorporates assortative mating for reproductive timing, a defining attribute of many aggregate breeding species. We demonstrate the utility of this framework by simulating a generalized salmonid lifecycle, varying input parameters, and comparing model outputs to theoretical expectations for several eco-evolutionary, population dynamic scenarios. Simulations with assortative mating systems resulted in more resilient and productive populations than those that were randomly mating. In accordance with established ecological and evolutionary theory, we also found that decreasing the magnitude of trait correlations, environmental variability, and strength of selection each had a positive effect on population growth. Our model is constructed in a modular framework so that future components can be easily added to address pressing issues such as the effects of supportive breeding, variable age structure, differential selection by sex or age, and fishery interactions on population growth and resilience. With code published in a public Github repository, model outputs may easily be tailored to specific study systems by parameterizing with empirically generated values from long-term ecological monitoring programs.
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Affiliation(s)
- Samuel A. May
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Jeffrey J. Hard
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington USA
| | - Michael J. Ford
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington USA
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Eric J. Ward
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington USA
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8
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [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: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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9
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Wadgymar SM, DeMarche ML, Josephs EB, Sheth SN, Anderson JT. Local adaptation: Causal agents of selection and adaptive trait divergence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022; 53:87-111. [PMID: 37790997 PMCID: PMC10544833 DOI: 10.1146/annurev-ecolsys-012722-035231] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation.
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Affiliation(s)
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Seema N Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602
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10
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Fidelity to Natal Tributary Streams by Kokanee Following Introduction to a Large Oligotrophic Reservoir. FISHES 2022. [DOI: 10.3390/fishes7030123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The WAC Bennett Dam was completed in 1968 and impounded the Upper Peace River to form the Williston Reservoir in north central British Columbia. In 1990, an enhancement project was initiated to stock Columbia River Kokanee (non-anadromous Sockeye Salmon; Oncorhynchus nerka) from southeastern British Columbia into tributary streams that drained into regions of the reservoir that were accessible by anglers. The current distribution of spawning Columbia-origin Kokanee in the Williston Reservoir watershed, however, does not reflect the locations where these fish were initially stocked and suggests extensive straying. Whether or not Kokanee will develop fidelity to specific spawning locations is not known, but it is important information to effectively manage these introduced fish. We used otolith microchemistry to estimate fidelity to natal streams by Columbia-origin Kokanee in the Williston Reservoir. Otolith elemental signatures for the region of the otolith that formed during the larval period and characterized the natal redd environment showed considerable variation among samples. Natal signatures tended to cluster for each river but not for all spawners, suggesting elemental signatures from other rivers. Homing to one of the four natal streams we examined was classified to be 73% based on linear discriminant analysis, although variation in the elemental signatures within each group suggests that homing by Kokanee to specific natal streams may be as low as 55%. Based on similarity of water elemental signatures for tributaries within large rivers, however, the proportion of fish that returned to their general region was likely higher and estimated to be approximately 83%. The result of regional homing could be reproductive isolation and adaptation to local conditions. It is unclear, however, if the current estimated level of straying will limit genetic differentiation and prevent local adaptation.
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11
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Makgae O, Moya A, Phaahlamohlaka T, Huang C, Coville N, Kirkland A, Liberti E. Direct visualisation of the surface atomic active sites of carbon-supported Co3O4 nanocrystals via high-resolution phase restoration. Chemphyschem 2022; 23:e202200031. [PMID: 35476226 PMCID: PMC9401059 DOI: 10.1002/cphc.202200031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/04/2022] [Indexed: 11/30/2022]
Abstract
The atomic arrangement of the terminating facets on spinel Co3O4 nanocrystals is strongly linked to their catalytic performance. However, the spinel crystal structure offers multiple possible surface terminations depending on the synthesis. Thus, understanding the terminating surface atomic structure is essential in developing high‐performance Co3O4 nanocrystals. In this work, we present direct atomic‐scale observation of the surface terminations of Co3O4 nanoparticles supported on hollow carbon spheres (HCSs) using exit wavefunction reconstruction from aberration‐corrected transmission electron microscopy focal‐series. The restored high‐resolution phases show distinct resolved oxygen and cobalt atomic columns. The data show that the structure of {100}, {110}, and {111} facets of spinel Co3O4 exhibit characteristic active sites for carbon monoxide (CO) adsorption, in agreement with density functional theory calculations. Of these facets, the {100} and {110} surface terminations are better suited for CO adsorption than the {111}. However, the presence of oxygen on the {111} surface termination indicates this facet also plays an essential role in CO adsorption. Our results demonstrate direct evidence of the surface termination atomic structure beyond the assumed stoichiometry of the surface.
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Affiliation(s)
- Ofentse Makgae
- Lund University, Centre for Analysis and Synthesis, Naturvetarvägen 14, P.O. Box 124, 221 00, Lund, SWEDEN
| | - Arthur Moya
- Oxford University: University of Oxford, Materials, UNITED KINGDOM
| | | | - Chen Huang
- Oxford University: University of Oxford, Materials, UNITED KINGDOM
| | - Neil Coville
- Wits University: University of the Witwatersrand, chemistry, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa, 2050, Johannesburg, South Africa, SOUTH AFRICA
| | - Angus Kirkland
- Oxford University: University of Oxford, Materials, 16 Parks Road, Oxford, University of Oxford, Oxford, OX1 3PH, Oxford, UNITED KINGDOM
| | - Emanuela Liberti
- Oxford University: University of Oxford, Materials, UNITED KINGDOM
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12
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Onley IR, Moseby KE, Austin JJ, Sherratt E. Morphological variation in skull shape and size across extinct and extant populations of the greater stick-nest rat (Leporillus conditor): implications for translocation. AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am21047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Fisher MC, Helser TE, Kang S, Gwak W, Canino MF, Hauser L. Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change. Ecol Evol 2022; 12:e8474. [PMID: 35127016 PMCID: PMC8794718 DOI: 10.1002/ece3.8474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine-scale connectivity in high gene flow marine species. When located at the equatorial edge of a species' range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species' range, by conducting restriction site-associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST = 0.025-0.042) and relatively small (Ne = 433-1,777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west-to-east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST ). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.
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Affiliation(s)
- Mary C. Fisher
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
- Present address:
School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Thomas E. Helser
- Resource Ecology and Fisheries Management DivisionAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashingtonUSA
| | - Sukyung Kang
- Fisheries Resources Management DivisionNational Institute of Fisheries ScienceBusanKorea
| | - Wooseok Gwak
- The Institute of Marine IndustryGyeongsang National UniversityTongyeongKorea
| | - Michael F. Canino
- Alaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashingtonUSA
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
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14
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Koch IJ, Narum SR. An evaluation of the potential factors affecting lifetime reproductive success in salmonids. Evol Appl 2021; 14:1929-1957. [PMID: 34429740 PMCID: PMC8372082 DOI: 10.1111/eva.13263] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 01/24/2023] Open
Abstract
Lifetime reproductive success (LRS), the number of offspring produced over an organism's lifetime, is a fundamental component of Darwinian fitness. For taxa such as salmonids with multiple species of conservation concern, understanding the factors affecting LRS is critical for the development and implementation of successful conservation management practices. Here, we reviewed the published literature to synthesize factors affecting LRS in salmonids including significant effects of hatchery rearing, life history, and phenotypic variation, and behavioral and spawning interactions. Additionally, we found that LRS is affected by competitive behavior on the spawning grounds, genetic compatibility, local adaptation, and hybridization. Our review of existing literature revealed limitations of LRS studies, and we emphasize the following areas that warrant further attention in future research: (1) expanding the range of studies assessing LRS across different life-history strategies, specifically accounting for distinct reproductive and migratory phenotypes; (2) broadening the variety of species represented in salmonid fitness studies; (3) constructing multigenerational pedigrees to track long-term fitness effects; (4) conducting LRS studies that investigate the effects of aquatic stressors, such as anthropogenic effects, pathogens, environmental factors in both freshwater and marine environments, and assessing overall body condition, and (5) utilizing appropriate statistical approaches to determine the factors that explain the greatest variation in fitness and providing information regarding biological significance, power limitations, and potential sources of error in salmonid parentage studies. Overall, this review emphasizes that studies of LRS have profoundly advanced scientific understanding of salmonid fitness, but substantial challenges need to be overcome to assist with long-term recovery of these keystone species in aquatic ecosystems.
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Affiliation(s)
- Ilana J. Koch
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
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15
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Prystupa S, McCracken GR, Perry R, Ruzzante DE. Population abundance in arctic grayling using genetics and close-kin mark-recapture. Ecol Evol 2021; 11:4763-4773. [PMID: 33976846 PMCID: PMC8093667 DOI: 10.1002/ece3.7378] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
Arctic Grayling (Thymallus arcticus) are among the most widely distributed and abundant freshwater fish in the Yukon Territory of Canada, yet little information exists regarding their broad and fine-scale population structures or the number and size of these populations. The estimation of population abundance is fundamental for robust management and conservation, yet estimating abundance in the wild is often difficult. Here, we estimated abundance of an Arctic Grayling population using multiple genetic markers and the close-kin mark-recapture (CKMR) method. A total of N = 1,104 Arctic Grayling collected from two systems in Yukon were genotyped at 38 sequenced microsatellites. We first identified structure and assessed genetic diversity (effective population size,N ^ e ). Collections from one of the systems (Lubbock River) comprised adults and young-of-the-year sampled independently allowing the identification of parent-offspring pairs (POPs), and thus, the estimation of abundance using CKMR. We used COLONY and CKMRsim to identify POPs and both provided similar results leading to indistinguishable estimates (95% CI) of census size, that is,N ^ c ( C O L O N Y ) = 1858 (1259-2457) andN ^ c ( C K M R s i m ) = 1812 (1229-2389). The accuracy of the population abundance estimates can in the future be improved with temporal sampling and more precise age or size-specific fecundity estimates for Arctic Grayling. Our study demonstrates that the method can be used to inform management and conservation policy for Arctic Grayling and likely also for other fish species for which the assumption of random and independent sampling of adults and offspring can be assured.
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Affiliation(s)
- Samuel Prystupa
- Department of BiologyDalhousie UniversityHalifaxNSCanada
- Present address:
Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | | | - Robert Perry
- Fish and Wildlife DivisionDepartment of EnvironmentWhitehorse, YukonCanada
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16
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Waters CD, Clemento A, Aykanat T, Garza JC, Naish KA, Narum S, Primmer CR. Heterogeneous genetic basis of age at maturity in salmonid fishes. Mol Ecol 2021; 30:1435-1456. [PMID: 33527498 DOI: 10.1111/mec.15822] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/07/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Anthony Clemento
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA.,Santa Cruz Laboratory, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - John Carlos Garza
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA.,Santa Cruz Laboratory, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Shawn Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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17
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Jian M, Zhao C, Li WX. Ligand Stabilized Ni 1 Catalyst for Efficient CO Oxidation. Chemphyschem 2020; 21:2417-2425. [PMID: 33063907 DOI: 10.1002/cphc.202000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/15/2020] [Indexed: 12/30/2022]
Abstract
Supported single transition metal (TM1 ) catalysts have attracted broad attention in academia recently. Still, their corresponding reactivity and stability under reaction conditions are critical but have not well explored at the fundamental level. Herein, we use density functional theory calculation and ab initio molecular dynamics simulation to investigate the role of reactants and ligands on the reactivity and stability of graphitic carbon nitride (g-C3 N4 ) supported Ni1 for CO oxidation. We find out that supported bare Ni1 atoms are only metastable on the surface and tend to diffuse into the interlayer of g-C3 N4 . Though Ni1 is catalytically active at moderate temperatures, CO adsorption induced dimerization deactivates the catalyst. Hydroxyl groups not only are able to stabilize the supported Ni1 atom, but also increase the reactivity by participating directly in the reaction. Our results provide valuable insights on improving the chemical stability of TM1 by ligands without sacrificing the reactivity, which are helpful for the rational design of highly loaded atomically dispersed supported metal catalysts.
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Affiliation(s)
- Minzhen Jian
- Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Chuanlin Zhao
- Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Wei-Xue Li
- Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
- Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, China
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18
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Barbraud C, Delord K. Selection against immigrants in wild seabird populations. Ecol Lett 2020; 24:84-93. [PMID: 33058398 DOI: 10.1111/ele.13624] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/12/2020] [Accepted: 09/22/2020] [Indexed: 11/30/2022]
Abstract
Immigration is a major demographic parameter shaping population dynamics and is an important driver of eco-evolutionary patterns, but the fitness consequences for individuals following their settlement to a new population (immigrants) remain poorly tested in wild animal populations, particularly among long-lived species. Here we show that immigrants have a lower fitness than residents in three wild seabird populations (wandering albatross Diomedea exulans, southern fulmar Fulmarus glacialoides, snow petrel Pagodroma nivea). Across all species and during a 32-year period, immigrants made on average -9 to 29% fewer breeding attempts, had 5-31% fewer fledglings, had 2-16% lower breeding success and produced 6-46% fewer recruits. Female immigration and male residency were also favored through differences in breeding performance. We provide evidence for selection against immigrants in wild populations of long-lived species and our results are consistent with female-biased dispersal in birds being driven by asymmetric limiting resources and the competitive ability of dispersers vs. non-dispersers.
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Affiliation(s)
- Christophe Barbraud
- Centre d'Etudes Biologiques de Chizé, CNRS UMR7372, Villiers en Bois, 79360, France
| | - Karine Delord
- Centre d'Etudes Biologiques de Chizé, CNRS UMR7372, Villiers en Bois, 79360, France
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19
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May SA, McKinney GJ, Hilborn R, Hauser L, Naish KA. Power of a dual-use SNP panel for pedigree reconstruction and population assignment. Ecol Evol 2020; 10:9522-9531. [PMID: 32953080 PMCID: PMC7487233 DOI: 10.1002/ece3.6645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 11/28/2022] Open
Abstract
The use of high-throughput, low-density sequencing approaches has dramatically increased in recent years in studies of eco-evolutionary processes in wild populations and domestication in commercial aquaculture. Most of these studies focus on identifying panels of SNP loci for a single downstream application, whereas there have been few studies examining the trade-offs for selecting panels of markers for use in multiple applications. Here, we detail the use of a bioinformatic workflow for the development of a dual-purpose SNP panel for parentage and population assignment, which included identifying putative SNP loci, filtering for the most informative loci for the two tasks, designing effective multiplex PCR primers, optimizing the SNP panel for performance, and performing quality control steps for downstream applications. We applied this workflow to two adjacent Alaskan Sockeye Salmon populations and identified a GTseq panel of 142 SNP loci for parentage and 35 SNP loci for population assignment. Only 50-75 panel loci were necessary for >95% accurate parentage, whereas population assignment success, with all 172 panel loci, ranged from 93.9% to 96.2%. Finally, we discuss the trade-offs and complexities of the decision-making process that drives SNP panel development, optimization, and testing.
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Affiliation(s)
- Samuel A. May
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Garrett J. McKinney
- NRC Research Associateship ProgramNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Ray Hilborn
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Kerry A. Naish
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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20
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Okamoto DK, Hessing-Lewis M, Samhouri JF, Shelton AO, Stier A, Levin PS, Salomon AK. Spatial variation in exploited metapopulations obscures risk of collapse. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02051. [PMID: 31820525 DOI: 10.1002/eap.2051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Unanticipated declines among exploited species have commonly occurred despite harvests that appeared sustainable prior to collapse. This is particularly true in the oceans where spatial scales of management are often mismatched with spatially complex metapopulations. We explore causes, consequences, and potential solutions for spatial mismatches in harvested metapopulations in three ways. First, we generate novel theory illustrating when and how harvesting metapopulations increases spatial variability and in turn masks local-scale volatility. Second, we illustrate why spatial variability in harvested metapopulations leads to negative consequences using an empirical example of a Pacific herring metapopulation. Finally, we construct a numerical management strategy evaluation model to identify and highlight potential solutions for mismatches in spatial scale and spatial variability. Our results highlight that spatial complexity can promote stability at large scales, however, ignoring spatial complexity produces cryptic and negative consequences for people and animals that interact with resources at small scales. Harvesting metapopulations magnifies spatial variability, which creates discrepancies between regional and local trends while increasing risk of local population collapses. Such effects asymmetrically impact locally constrained fishers and predators, which are more exposed to risks of localized collapses. Importantly, we show that dynamically optimizing harvest can minimize local risk without sacrificing yield. Thus, multiple nested scales of management may be necessary to avoid cryptic collapses in metapopulations and the ensuing ecological, social, and economic consequences.
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Affiliation(s)
- Daniel K Okamoto
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida, 32303, USA
- Hakai Institute, Hyacinthe Bay Road, Quadra Island, Vancouver, British Columbia, V0P 1H0, Canada
- School of Resource and Environmental Management, Simon Fraser University, 643A Science Road, Burnaby, British Columbia, V5A 1S6, Canada
| | - Margot Hessing-Lewis
- Hakai Institute, Hyacinthe Bay Road, Quadra Island, Vancouver, British Columbia, V0P 1H0, Canada
| | - Jameal F Samhouri
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard East, Seattle, Washington, 98112, USA
| | - Andrew O Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard East, Seattle, Washington, 98112, USA
| | - Adrian Stier
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, 93106, USA
| | - Philip S Levin
- The Nature Conservancy, 74 Wall Street, Seattle, California, 98121, USA
- School of Environment and Forestry Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Anne K Salomon
- Hakai Institute, Hyacinthe Bay Road, Quadra Island, Vancouver, British Columbia, V0P 1H0, Canada
- School of Resource and Environmental Management, Simon Fraser University, 643A Science Road, Burnaby, British Columbia, V5A 1S6, Canada
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21
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22
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Clucas GV, Lou RN, Therkildsen NO, Kovach AI. Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing. Evol Appl 2019; 12:1971-1987. [PMID: 31700539 PMCID: PMC6824067 DOI: 10.1111/eva.12861] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/14/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022] Open
Abstract
Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome-wide patterns of variation, we used low-coverage sequencing to perform a region-wide, whole-genome analysis of fine-scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole-genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter- and spring-spawning populations revealed highly elevated relative (FST ) and absolute (dxy ) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain-pituitary-gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high-resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome-scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.
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Affiliation(s)
- Gemma V. Clucas
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - R. Nicolas Lou
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | | | - Adrienne I. Kovach
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
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23
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McConnell CJ, Atkinson S, Oxman D, Westley PAH. Is blood cortisol or vateritic otolith composition associated with natal dispersal or reproductive performance on the spawning grounds of straying and homing hatchery-produced chum salmon ( Oncorhynchus keta) in Southeast Alaska? Biol Open 2019; 8:bio.042853. [PMID: 31182627 PMCID: PMC6602324 DOI: 10.1242/bio.042853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Homing with high fidelity to natal spawning grounds for reproduction is a hallmark of anadromous Pacific salmon biology, although low rates of dispersal (‘straying’) also occurs. Currently little is known about the proximate factors influencing straying, which limits our understanding of this fundamental biological phenomenon and impedes options for reducing straying-mediated interactions between wild and hatchery-produced individuals. We explored the potential role of stress experienced in captivity prior to intentional release to manifest in developmental irregularities and potentially influence rates of straying by adults. We compared two proxies for stress between groups of hatchery-produced individuals that had homed back to the hatchery or strayed to non-natal streams compared to wild individuals that were presumed to have homed to a wild spawning stream. Blood plasma cortisol was used to assess stress at the terminus of their migration, and percent frequency of vateritic otolith development within groups as a measure of stresses incurred during development. We found no evidence that either proxy for stress was associated with straying. No differences in cortisol concentrations were found between wild and hatchery-produced chum salmon that had homed or strayed, either in males (wild=95.9±175.7 ng/ml; stray=113.4±99.7 ng/ml; home=124.7±113.8 ng/ml) or females (wild=307.6±83.4 ng/ml; stray= 329.0±208.9 ng/ml; home=294.1±134.8 ng/ml); however, significant differences between males and females occurred in each group. The percent frequency of vaterite occurrence in otoliths of hatchery-produced chum salmon that either strayed (40% vaterite) or homed (45% vaterite) did not differ significantly, though rates of vaterite occurred less frequently in wild chum salmon (24%), which is consistent with other studies. Mass thermal marking of juvenile fish in hatcheries is unlikely to increase vateritic development as neither intensity (number of temperature changes) or complexity (number of temperature change sequences) of the mark was associated with frequency of vaterite occurrence. Though not associated with straying, cortisol concentrations were associated with shorter instream lifespan of both hatchery and wild individuals but did not appear to influence rates of egg retention in spawning females, suggesting an equivocal role in reproductive ecology. Our results are suggestive that stress induced during the early stages of rearing in a hatchery environment from marking or other causes may not increase straying later in life, though the higher rates of vaterite observed in hatchery-produced fish may come at a cost of increased marine mortality, due to the otoliths' role in navigation and hearing. Summary: Straying mediates ecological interactions and gene flow between salmon populations. Understanding physiological controls and underlying causes of straying by hatchery-produced salmon may help managers minimize deleterious interactions.
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Affiliation(s)
- Casey J McConnell
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 323 Garteeni Hwy, Hoonah, AK 99829, USA
| | - Shannon Atkinson
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Lena Point Loop Road, Juneau, AK 99801, USA
| | - Dion Oxman
- Alaska Department of Fish and Game, 10107 Bentwood Pl, Juneau, AK 9901, USA
| | - Peter A H Westley
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 905. N Koyukuk Drive, Fairbanks, AK 99775, USA
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24
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Clucas GV, Kerr LA, Cadrin SX, Zemeckis DR, Sherwood GD, Goethel D, Whitener Z, Kovach A. Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank. PLoS One 2019; 14:e0216992. [PMID: 31125344 PMCID: PMC6534298 DOI: 10.1371/journal.pone.0216992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 05/02/2019] [Indexed: 12/15/2022] Open
Abstract
Atlantic cod (Gadus morhua) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.
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Affiliation(s)
- G. V. Clucas
- Department of Natural Resources, University of New Hampshire, Durham, NH, United States of America
| | - L. A. Kerr
- Gulf of Maine Research Institute, Portland, ME, United States of America
| | - S. X. Cadrin
- School for Marine Science & Technology, University of Massachusetts Dartmouth, New Bedford, MA, United States of America
| | - D. R. Zemeckis
- Department of Agriculture and Natural Resources, Rutgers University, Toms River, NJ, United States of America
| | - G. D. Sherwood
- Gulf of Maine Research Institute, Portland, ME, United States of America
| | - D. Goethel
- F/V Ellen Diane, Hampton, NH, United States of America
| | - Z. Whitener
- Gulf of Maine Research Institute, Portland, ME, United States of America
| | - A.I. Kovach
- Department of Natural Resources, University of New Hampshire, Durham, NH, United States of America
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25
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Larson WA, Dann TH, Limborg MT, McKinney GJ, Seeb JE, Seeb LW. Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska. Mol Ecol 2019; 28:2254-2271. [DOI: 10.1111/mec.15082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/21/2019] [Accepted: 03/20/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Wesley A. Larson
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Tyler H. Dann
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
- Gene Conservation Laboratory Alaska Department of Fish and Game Anchorage Alaska
| | - Morten T. Limborg
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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26
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Yeakel JD, Gibert JP, Gross T, Westley PAH, Moore JW. Eco-evolutionary dynamics, density-dependent dispersal and collective behaviour: implications for salmon metapopulation robustness. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0018. [PMID: 29581402 PMCID: PMC5882987 DOI: 10.1098/rstb.2017.0018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 11/12/2022] Open
Abstract
The spatial dispersal of individuals plays an important role in the dynamics of populations, and is central to metapopulation theory. Dispersal provides connections within metapopulations, promoting demographic and evolutionary rescue, but may also introduce maladapted individuals, potentially lowering the fitness of recipient populations through introgression of heritable traits. To explore this dual nature of dispersal, we modify a well-established eco-evolutionary model of two locally adapted populations and their associated mean trait values, to examine recruiting salmon populations that are connected by density-dependent dispersal, consistent with collective migratory behaviour that promotes navigation. When the strength of collective behaviour is weak such that straying is effectively constant, we show that a low level of straying is associated with the highest gains in metapopulation robustness and that high straying serves to erode robustness. Moreover, we find that as the strength of collective behaviour increases, metapopulation robustness is enhanced, but this relationship depends on the rate at which individuals stray. Specifically, strong collective behaviour increases the presence of hidden low-density basins of attraction, which may serve to trap disturbed populations, and this is exacerbated by increased habitat heterogeneity. Taken as a whole, our findings suggest that density-dependent straying and collective migratory behaviour may help metapopulations, such as in salmon, thrive in dynamic landscapes. Given the pervasive eco-evolutionary impacts of dispersal on metapopulations, these findings have important ramifications for the conservation of salmon metapopulations facing both natural and anthropogenic contemporary disturbances.This article is part of the theme issue 'Collective movement ecology'.
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Affiliation(s)
- Justin D Yeakel
- School of Natural Sciences, University of California, Merced, CA 95340, USA .,The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Jean P Gibert
- School of Natural Sciences, University of California, Merced, CA 95340, USA
| | - Thilo Gross
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TH, UK
| | - Peter A H Westley
- Department of Fisheries, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Jonathan W Moore
- Earth2Oceans Research Group, Simon Fraser University, Burnaby BC, Canada V5A 1S6
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27
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Mobley KB, Granroth-Wilding H, Ellmen M, Vähä JP, Aykanat T, Johnston SE, Orell P, Erkinaro J, Primmer CR. Home ground advantage: Local Atlantic salmon have higher reproductive fitness than dispersers in the wild. SCIENCE ADVANCES 2019; 5:eaav1112. [PMID: 30820455 PMCID: PMC6392789 DOI: 10.1126/sciadv.aav1112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/14/2019] [Indexed: 05/04/2023]
Abstract
A long-held, but poorly tested, assumption in natural populations is that individuals that disperse into new areas for reproduction are at a disadvantage compared to individuals that reproduce in their natal habitat, underpinning the eco-evolutionary processes of local adaptation and ecological speciation. Here, we capitalize on fine-scale population structure and natural dispersal events to compare the reproductive success of local and dispersing individuals captured on the same spawning ground in four consecutive parent-offspring cohorts of wild Atlantic salmon (Salmo salar). Parentage analysis conducted on adults and juvenile fish showed that local females and males had 9.6 and 2.9 times higher reproductive success than dispersers, respectively. Our results reveal how higher reproductive success in local spawners compared to dispersers may act in natural populations to drive population divergence and promote local adaptation over microgeographic spatial scales without clear morphological differences between populations.
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Affiliation(s)
- Kenyon B. Mobley
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
- Corresponding author.
| | - Hanna Granroth-Wilding
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
- Department of Biology, University of Turku, Finland, Itäinen 10 Pitkäkatu 4, Turku FI-20520, Finland
| | - Mikko Ellmen
- Department of Biology, University of Turku, Finland, Itäinen 10 Pitkäkatu 4, Turku FI-20520, Finland
| | - Juha-Pekka Vähä
- Association for Water and Environment of Western Uusimaa, P.O. Box 51, FI-08101, Lohja, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Susan E. Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Panu Orell
- Natural Resources Institute Finland (Luke), P.O. Box 413, FI-90014 Oulu, Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland (Luke), P.O. Box 413, FI-90014 Oulu, Finland
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
- Institute for Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science, University of Helsinki, 00014 Helsinki, Finland
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Oke KB, Motivans E, Quinn TP, Hendry AP. Sexual dimorphism modifies habitat‐associated divergence: Evidence from beach and creek breeding sockeye salmon. J Evol Biol 2018; 32:227-242. [DOI: 10.1111/jeb.13407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Krista B. Oke
- Department of Biology and Redpath Museum McGill University Montreal Quebec Canada
- College of Fisheries and Ocean Sciences University of Alaska Fairbanks Juneau Alaska
| | - Elena Motivans
- Department of Biology and Redpath Museum McGill University Montreal Quebec Canada
- Helmholtz Centre for Environmental Research Leipzig Germany
| | - Thomas P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Andrew P. Hendry
- Department of Biology and Redpath Museum McGill University Montreal Quebec Canada
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Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations. Proc Natl Acad Sci U S A 2018; 116:177-186. [PMID: 30514813 DOI: 10.1073/pnas.1811559115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.
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30
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Dedrick AG, Baskett ML. Integrating Genetic and Demographic Effects of Connectivity on Population Stability: The Case of Hatchery Trucking in Salmon. Am Nat 2018; 192:E62-E80. [PMID: 30016162 DOI: 10.1086/697581] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Connectivity among populations can have counteracting effects on population stability. Demographically, connectivity can rescue local populations but increase the synchrony across populations. Genetically, connectivity can counteract drift locally but homogenize genotypes across populations. Population independence and diversity underlies system-level buffering against environmental variability, termed the portfolio effect. The portfolio effect has declined in California fall-run Chinook salmon, possibly in part because of the trucking of juvenile hatchery-reared fish for downstream release, which reduces juvenile mortality but increases the connectivity between rivers. We use a dynamical population model to test whether this increased connectivity can explain the loss of the portfolio effect and quantify the relative demographic and genetic contributions to portfolio effect erosion. In the model, populations experience different within-population environmental conditions and the same time-variable ocean conditions, the response to which can depend on a quantitative genetic trait. We find that increased trucking for one population's hatchery can lead to a loss of the portfolio effect, with a system-level trade-off between increased average abundance and increased variability in abundance. This trade-off is much stronger when we include the effects of genetic homogenization than when we consider demographic synchronization alone. Therefore, genetic homogenization can outweigh demographic synchrony in determining the system-level effect of connectivity.
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31
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Gentili R, Solari A, Diekmann M, Duprè C, Monti GS, Armiraglio S, Assini S, Citterio S. Genetic differentiation, local adaptation and phenotypic plasticity in fragmented populations of a rare forest herb. PeerJ 2018; 6:e4929. [PMID: 29915689 PMCID: PMC6004105 DOI: 10.7717/peerj.4929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/18/2018] [Indexed: 12/04/2022] Open
Abstract
Background Due to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range. Methods For each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (FST) and quantitative (PST) genetic differentiation of populations. Results The populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed PST < FST, indicating convergent selection. Discussion The variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors.
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Affiliation(s)
- Rodolfo Gentili
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Aldo Solari
- Department of Economics, Management and Statistics, University of Milan-Bicocca, Milan, Italy
| | | | - Cecilia Duprè
- Institute of Ecology, University of Bremen, Bremen, Germany
| | - Gianna Serafina Monti
- Department of Economics, Management and Statistics, University of Milan-Bicocca, Milan, Italy
| | | | - Silvia Assini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Sandra Citterio
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
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32
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Pires THS, Borghezan EA, Machado VN, Powell DL, Röpke CP, Oliveira C, Zuanon J, Farias IP. Testing Wallace's intuition: water type, reproductive isolation and divergence in an Amazonian fish. J Evol Biol 2018; 31:882-892. [PMID: 29577482 DOI: 10.1111/jeb.13272] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 01/20/2023]
Abstract
Alfred Russel Wallace proposed classifying Amazon rivers based on their colour and clarity: white, black and clear water. Wallace also proposed that black waters could mediate diversification and yield distinct fish species. Here, we bring evidence of speciation mediated by water type in the sailfin tetra (Crenuchus spilurus), a fish whose range encompasses rivers of very distinct hydrochemical conditions. Distribution of the two main lineages concords with Wallace's water types: one restricted to the acidic and nutrient-poor waters of the Negro River (herein Rio Negro lineage) and a second widespread throughout the remaining of the species' distribution (herein Amazonas lineage). These lineages occur over a very broad geographical range, suggesting that despite occurring in regions separated by thousands of kilometres, individuals of the distinct lineages fail to occupy each other's habitats, hundreds of metres apart and not separated by physical barrier. Reproductive isolation was assessed in isolated pairs exposed to black-water conditions. All pairs with at least one individual of the lineage not native to black waters showed significantly lower spawning success, suggesting that the water type affected the fitness and contributed to reproductive isolation. Our results endorse Wallace's intuition and highlight the importance of ecological factors in shaping diversity of the Amazon fish fauna.
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Affiliation(s)
- Tiago H S Pires
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Elio A Borghezan
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Valeria N Machado
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | - Daniel L Powell
- Department of Biology, Texas A&M University. TAMU, College Station, TX, USA
| | - Cristhiana P Röpke
- Departamento de Ciências Pesqueiras, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Jansen Zuanon
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
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33
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Lin JE, Hard JJ, Hilborn R, Hauser L. Modeling local adaptation and gene flow in sockeye salmon. Ecosphere 2017. [DOI: 10.1002/ecs2.2039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jocelyn E. Lin
- School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
| | - Jeffrey J. Hard
- Conservation Biology Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2725 Montlake Boulevard East Seattle Washington 98112 USA
| | - Ray Hilborn
- School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences University of Washington Box 355020 Seattle Washington 98195 USA
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34
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Samuk K, Owens GL, Delmore KE, Miller SE, Rennison DJ, Schluter D. Gene flow and selection interact to promote adaptive divergence in regions of low recombination. Mol Ecol 2017; 26:4378-4390. [DOI: 10.1111/mec.14226] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/02/2017] [Accepted: 06/13/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Kieran Samuk
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Gregory L. Owens
- Department of Botany; University of British Columbia; Vancouver BC Canada
| | | | - Sara E. Miller
- Department of Neurobiology and Behavior; Cornell University; Ithaca NY USA
| | - Diana J. Rennison
- Institut fur Okologie und Evolution; Universitat Bern; Bern Switzerland
| | - Dolph Schluter
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
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35
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After 100 years: hydroelectric dam-induced life-history divergence and population genetic changes in sockeye salmon (Oncorhynchus nerka). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0992-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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36
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Kaufmann J, Lenz TL, Kalbe M, Milinski M, Eizaguirre C. A field reciprocal transplant experiment reveals asymmetric costs of migration between lake and river ecotypes of three-spined sticklebacks (Gasterosteus aculeatus
). J Evol Biol 2017; 30:938-950. [DOI: 10.1111/jeb.13057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022]
Affiliation(s)
- J. Kaufmann
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
- DEE; University of Lausanne; Lausanne Switzerland
| | - T. L. Lenz
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - M. Kalbe
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - M. Milinski
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - C. Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- School of Biological and Chemical Sciences; Queen Mary University of London; London UK
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37
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Larson WA, Limborg MT, McKinney GJ, Schindler DE, Seeb JE, Seeb LW. Genomic islands of divergence linked to ecotypic variation in sockeye salmon. Mol Ecol 2016; 26:554-570. [PMID: 27864910 DOI: 10.1111/mec.13933] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 10/14/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with FST > 0.14 (average FST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80-402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.
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Affiliation(s)
- Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Daniel E Schindler
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
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Shenoi VN, Prasad NG. Local adaptation to developmental density does not lead to higher mating success in Drosophila melanogaster. J Evol Biol 2016; 29:2036-2042. [PMID: 27353197 DOI: 10.1111/jeb.12927] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/19/2016] [Accepted: 06/24/2016] [Indexed: 01/18/2023]
Abstract
In this study, we investigate the effect of local adaptation to developmental density on male mating success in laboratory populations of Drosophila melanogaster. Mating success is known to be influenced by body condition which can in turn be influenced by local adaptation. We test the hypothesis that males adapted to a given environment have higher mating success when assayed in that environment. We used males selected for adaptation to high larval density and their controls which are reared at low larval density. We grew assay males in low and high densities whereas the focal females (raised at low larval density) used for the experiment belonged to the common ancestor of selected and control populations. We considered selected males grown at high density and control males grown at low density as 'adapted'. Similarly, we considered selected males grown at low density and control males grown at high density as 'nonadapted'. Selected male belonging to a given treatment (larval density) was made to compete with control male of the same treatment for mating with ancestral female. We quantified components of reproductive fitness: mating latency, copulation duration, mating success and number of progeny sired by the 'adapted' and 'nonadapted' males. The results show that local adaptation does not lead to higher mating success in populations adapted to their own larval rearing environment.
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Affiliation(s)
- V N Shenoi
- Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - N G Prasad
- Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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39
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Camacho C, Sáez P, Sánchez S, Palacios S, Molina C, Potti J. The road to opportunities: landscape change promotes body-size divergence in a highly mobile species. Curr Zool 2016; 62:7-14. [PMID: 29491885 PMCID: PMC5804134 DOI: 10.1093/cz/zov008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/23/2015] [Indexed: 11/16/2022] Open
Abstract
Landscape change provides a suitable framework for investigating population-level responses to novel ecological pressures. However, relatively little attention has been paid to examine the potential influence of landscape change on the geographic scale of population differentiation. Here, we tested for morphological differentiation of red-necked nightjars Caprimulgus ruficollis breeding in a managed property and a natural reserve situated less than 10 km apart. At both sites, we also estimated site fidelity over 5 years and quantified the potential foraging opportunities for nightjars. Breeding birds in the managed habitat were significantly larger in size—as indexed by keel length—than those in the natural one. However, there were no significant differences in wing or tail length. Immigration from neighboring areas was almost negligible and, furthermore, no individual (out of 1130 captures overall) exchanged habitats between years, indicating strong site fidelity. Food supply for nightjars was equally abundant in both habitats, but the availability of foraging sites was remarkably higher in the managed property. As a result, nightjars—particularly fledglings—in the latter habitat benefited from increased foraging opportunities in relation to those in the natural site. It seems likely that the fine-scale variation in nightjar morphology reflects a phenotypic response to unequal local conditions, since non-random dispersal or differential mortality had been determined not to be influential. High site fidelity appears to contribute to the maintenance of body-size differences between the two habitats. Results from this nightjar population highlight the potential of human-induced landscape change to promote population-level responses at exceedingly small geographic scales.
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Affiliation(s)
- Carlos Camacho
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain
| | - Pedro Sáez
- Department of Environmental Biology and Public Health. University of Huelva. Av. Andalucía, 21071 Huelva, Spain
| | - Sonia Sánchez
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain
| | - Sebastián Palacios
- Department of Conservation Biology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain, and
| | - Carlos Molina
- Sociedad Española de Ornitología. Centro Ornitológico Francisco Bernis. Paseo Marismeño sn, 21750 Huelva, Spain
| | - Jaime Potti
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio, 41092 Seville, Spain
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40
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Westley PAH, Dittman AH, Ward EJ, Quinn TP. Signals of climate, conspecific density, and watershed features in patterns of homing and dispersal by Pacific salmon. Ecology 2016; 96:2823-33. [PMID: 26649402 DOI: 10.1890/14-1630.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It is widely assumed that rates of dispersal in animal populations are plastic in response to intrinsic and extrinsic cues, yet the factors influencing this plasticity are rarely known. This knowledge gap is surprising given the important role of dispersal in facilitating range shifts that may allow populations to persist in a rapidly changing global climate. We used two decades of tagging and recapture data from 19 hatchery populations of Oncorhynchus tshawytscha (Chinook salmon) in the Columbia River, USA, to quantify the effects of regional and local climate conditions, density dependence, watershed features such as area and position on the landscape, and direct anthropogenic influence on dispersal rates by adult salmon during the breeding season. We found that the probability of dispersal, termed "straying" in salmon, is plastic in'response to multiple factors and that populations showed varied responses that were largely idiosyncratic. A regional climate index (Pacific Decadal Oscillation), water temperatures in the mainstem Columbia River that was commonly experience by populations during migration, water temperatures in local subbasins unique to each population during the breeding season, migration distance, and density dependence had the strongest effects on dispersal. Patterns of dispersal plasticity in response to commonly experienced conditions were consistent with gene by environment interactions, though we are tentative about this interpretation given the domesticated history of these populations. Overall, our results warn against attempts to predict future range shifts of migratory species without considering population-specific dispersal plasticity, and also caution against the use of few populations to infer species-level patterns. Ultimately, our results provide evidence that analyses that examine the response of dispersal to single factors may be misleading.
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41
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Berdahl A, van Leeuwen A, Levin SA, Torney CJ. Collective behavior as a driver of critical transitions in migratory populations. MOVEMENT ECOLOGY 2016; 4:18. [PMID: 27429757 PMCID: PMC4946155 DOI: 10.1186/s40462-016-0083-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/19/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Mass migrations are among the most striking examples of animal movement in the natural world. Such migrations are major drivers of ecosystem processes and strongly influence the survival and fecundity of individuals. For migratory animals, a formidable challenge is to find their way over long distances and through complex, dynamic environments. However, recent theoretical and empirical work suggests that by traveling in groups, individuals are able to overcome these challenges and increase their ability to navigate. Here we use models to explore the implications of collective navigation on migratory, and population, dynamics, for both breeding migrations (to-and-fro migrations between distinct, fixed, end-points) and feeding migrations (loop migrations that track favorable conditions). RESULTS We show that while collective navigation does improve a population's ability to migrate accurately, it can lead to Allee effects, causing the sudden collapse of populations if numbers fall below a critical threshold. In some scenarios, hysteresis prevents the migration from recovering even after the cause of the collapse has been removed. In collectively navigating populations that are locally adapted to specific breeding sites, a slight increase in mortality can cause a collapse of genetic population structure, rather than population size, making it more difficult to detect and prevent. CONCLUSIONS Despite the large interest in collective behavior and its ubiquity in many migratory species, there is a notable lack of studies considering the implications of social navigation on the ecological dynamics of migratory species. Here we highlight the potential for a previously overlooked Allee effect in socially migrating species that may be important for conservation and management of such species.
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Affiliation(s)
- Andrew Berdahl
- />Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, 87501 NM USA
- />Department of Ecology & Evolutionary Biology, Princeton University, Princeton, 08544 NJ USA
| | - Anieke van Leeuwen
- />Department of Ecology & Evolutionary Biology, Princeton University, Princeton, 08544 NJ USA
| | - Simon A. Levin
- />Department of Ecology & Evolutionary Biology, Princeton University, Princeton, 08544 NJ USA
| | - Colin J. Torney
- />Department of Ecology & Evolutionary Biology, Princeton University, Princeton, 08544 NJ USA
- />Centre for Mathematics and the Environment, University of Exeter, Penryn Campus, Cornwall, UK
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42
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Armstrong JB, Ward EJ, Schindler DE, Lisi PJ. Adaptive capacity at the northern front: sockeye salmon behaviourally thermoregulate during novel exposure to warm temperatures. CONSERVATION PHYSIOLOGY 2016; 4:cow039. [PMID: 27729980 PMCID: PMC5055284 DOI: 10.1093/conphys/cow039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 05/18/2023]
Abstract
As climate change increases maximal water temperatures, behavioural thermoregulation may be crucial for the persistence of coldwater fishes, such as salmonids. Although myriad studies have documented behavioural thermoregulation in southern populations of salmonids, few if any have explored this phenomenon in northern populations, which are less likely to have an evolutionary history of heat stress, yet are predicted to experience substantial warming. Here, we treated a rare heat wave as a natural experiment to test whether wild sockeye salmon (Oncorhynchus nerka) at the northern extent of their primary range (60° latitude) can thermoregulate in response to abnormally high thermal conditions. We tagged adult sockeye salmon with temperature loggers as they staged in a lake epilimnion prior to spawning in small cold streams (n = 40 recovered loggers). As lake surface temperatures warmed to physiologically suboptimal levels (15-20°C), sockeye salmon thermoregulated by moving to tributary plumes or the lake metalimnion. A regression of fish body temperature against lake surface temperature indicated that fish moved to cooler waters when the epilimnion temperature exceeded ~12°C. A bioenergetics model suggested that the observed behaviour reduced daily metabolic costs by as much as ~50% during the warmest conditions (18-20°C). These results provide rare evidence of cool-seeking thermoregulation at the poleward extent of a species range, emphasizing the potential ubiquity of maximal temperature constraints and the functional significance of thermal heterogeneity for buffering poikilotherms from climate change.
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Affiliation(s)
- Jonathan B. Armstrong
- Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331,USA
- Corresponding author:Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR 97331, USA. Tel: +1-541-840-6017.
| | - Eric J. Ward
- Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard East, Seattle, WA 98112,USA
| | - Daniel E. Schindler
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98105,USA
| | - Peter J. Lisi
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98105,USA
- Center for Limnology, University of Wisconsin, 680 North Park Street, Madison, WI 53706,USA
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43
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Peterson DA, Hilborn R, Hauser L. Exploratory behavior of dispersers within a metapopulation of sockeye salmon. Behav Ecol 2015. [DOI: 10.1093/beheco/arv129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Berdahl A, Torney CJ, Schertzer E, Levin SA. On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments. Evolution 2015; 69:1390-1405. [DOI: 10.1111/evo.12664] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 04/07/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Berdahl
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
- Santa Fe Institute; Santa Fe New Mexico 87501
| | - Colin J. Torney
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
- Centre for Mathematics and the Environment; University of Exeter; Penryn Campus Cornwall United Kingdom
| | - Emmanuel Schertzer
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
- Laboratoire de Probabilités et Modèles Aléatoires des Universités Pierre et Marie Curie et Denis Diderot; Paris France
- Collège de France; Center for Interdisciplinary Research in Biology CNRS UMR 7241; Paris France
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
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45
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Young EF, Belchier M, Hauser L, Horsburgh GJ, Meredith MP, Murphy EJ, Pascoal S, Rock J, Tysklind N, Carvalho GR. Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species. Evol Appl 2015; 8:486-509. [PMID: 26029262 PMCID: PMC4430772 DOI: 10.1111/eva.12259] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/27/2015] [Indexed: 01/27/2023] Open
Abstract
Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.
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Affiliation(s)
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Gavin J Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | | | | | - Sonia Pascoal
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
| | - Jennifer Rock
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK ; School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Department of Zoology, University of Otago Dunedin, 9054, New Zealand
| | - Niklas Tysklind
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Campus Agronomique BP 709-97387, Kourou Cedex, France
| | - Gary R Carvalho
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
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46
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Christie MR, Knowles LL. Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes. Evol Appl 2015; 8:454-63. [PMID: 26029259 PMCID: PMC4430769 DOI: 10.1111/eva.12255] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/16/2015] [Indexed: 01/16/2023] Open
Abstract
Corridors are frequently proposed to connect patches of habitat that have become isolated due to human-mediated alterations to the landscape. While it is understood that corridors can facilitate dispersal between patches, it remains unknown whether corridors can mitigate the negative genetic effects for entire communities modified by habitat fragmentation. These negative genetic effects, which include reduced genetic diversity, limit the potential for populations to respond to selective agents such as disease epidemics and global climate change. We provide clear evidence from a forward-time, agent-based model (ABM) that corridors can facilitate genetic resilience in fragmented habitats across a broad range of species dispersal abilities and population sizes. Our results demonstrate that even modest increases in corridor width decreased the genetic differentiation between patches and increased the genetic diversity and effective population size within patches. Furthermore, we document a trade-off between corridor quality and corridor design whereby populations connected by high-quality habitat (i.e., low corridor mortality) are more resilient to suboptimal corridor design (e.g., long and narrow corridors). The ABM also revealed that species interactions can play a greater role than corridor design in shaping the genetic responses of populations to corridors. These results demonstrate how corridors can provide long-term conservation benefits that extend beyond targeted taxa and scale up to entire communities irrespective of species dispersal abilities or population sizes.
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Affiliation(s)
- Mark R Christie
- Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA ; Department of Biological Sciences & Department of Forestry and Natural Resources, Purdue University West Lafayette, IN, USA
| | - L Lacey Knowles
- Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
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47
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Ford MJ, Murdoch A, Hughes M. Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha). Mol Ecol 2015; 24:1109-21. [DOI: 10.1111/mec.13091] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 01/19/2015] [Accepted: 01/21/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Michael J. Ford
- Northwest Fisheries Science Center; National Marine Fisheries Service; 2725 Montlake Blvd E Seattle WA 98112 USA
| | - Andrew Murdoch
- Washington Department of Fish and Wildlife; 3515 Chelan Highway 97A Wenatchee WA 98801 USA
| | - Michael Hughes
- Washington Department of Fish and Wildlife; 3515 Chelan Highway 97A Wenatchee WA 98801 USA
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48
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Lemay MA, Russello MA. Genetic evidence for ecological divergence in kokanee salmon. Mol Ecol 2015; 24:798-811. [PMID: 25580953 DOI: 10.1111/mec.13066] [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: 05/05/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 01/16/2023]
Abstract
The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of nonmodel organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines); however, outside of the spawning season the two ecotypes co-occur in many lakes and lack diagnostic morphological characteristics. We used restriction site-associated DNA (RAD) sequencing to identify 6145 SNPs and genotype kokanee from multiple spawning sites in Okanagan Lake (British Columbia, Canada). Outlier tests revealed 18 loci putatively under divergent selection between ecotypes, all of which exhibited temporally stable allele frequencies within ecotypes. Six outliers were annotated to sequences in the NCBI database, two of which matched genes associated with early development. There was no evidence for neutral genetic differentiation; however, outlier loci demonstrated significant structure with respect to ecotype and had high assignment accuracy in mixed composition simulations. The absence of neutral structure combined with a small number of highly divergent outlier loci is consistent with theoretical predictions for the early stages of ecological divergence. These outlier loci were then applied to a realistic fisheries scenario in which additional RAD sequencing was used to genotype kokanee collected by trawl in Okanagan Lake, providing preliminary evidence that this approach may be an effective tool for conservation and management.
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Affiliation(s)
- Matthew A Lemay
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, British Columbia, Canada, V1V 1V7
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49
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Larson WA, Seeb JE, Dann TH, Schindler DE, Seeb LW. Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon. Mol Ecol 2014; 23:5448-61. [DOI: 10.1111/mec.12949] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Wesley A. Larson
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle WA 98195-5020 USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle WA 98195-5020 USA
| | - Tyler H. Dann
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle WA 98195-5020 USA
- Gene Conservation Laboratory; Alaska Department of Fish and Game; 333 Raspberry Road Anchorage AK 99518 USA
| | - Daniel E. Schindler
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle WA 98195-5020 USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle WA 98195-5020 USA
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50
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Bentley KT, Schindler DE, Cline TJ, Armstrong JB, Macias D, Ciepiela LR, Hilborn R. Predator avoidance during reproduction: diel movements by spawning sockeye salmon between stream and lake habitats. J Anim Ecol 2014; 83:1478-89. [DOI: 10.1111/1365-2656.12223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/31/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Kale T. Bentley
- School of Aquatic and Fishery Sciences; University of Washington; Box 355020 Seattle WA USA
| | - Daniel E. Schindler
- School of Aquatic and Fishery Sciences; University of Washington; Box 355020 Seattle WA USA
| | - Timothy J. Cline
- School of Aquatic and Fishery Sciences; University of Washington; Box 355020 Seattle WA USA
| | - Jonathan B. Armstrong
- School of Aquatic and Fishery Sciences; University of Washington; Box 355020 Seattle WA USA
- Wyoming Cooperative Fish and Wildlife Research Unit; Department of Zoology and Physiology; University of Wyoming; Laramie WY 82071 USA
| | - Daniel Macias
- Department of Fish, Wildlife and Conservation Ecology; New Mexico State University; Box 30003 Las Cruces NM USA
| | - Lindsy R. Ciepiela
- School of Aquatic and Fishery Sciences; University of Washington; Box 355020 Seattle WA USA
| | - Ray Hilborn
- School of Aquatic and Fishery Sciences; University of Washington; Box 355020 Seattle WA USA
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