1
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Schmid M, Rueffler C, Lehmann L, Mullon C. Resource Variation Within and Between Patches: Where Exploitation Competition, Local Adaptation, and Kin Selection Meet. Am Nat 2024; 203:E19-E34. [PMID: 38207145 DOI: 10.1086/727483] [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] [Indexed: 01/13/2024]
Abstract
AbstractIn patch- or habitat-structured populations, different processes can favor adaptive polymorphism at different scales. While spatial heterogeneity can generate spatially disruptive selection favoring variation between patches, local competition can lead to locally disruptive selection promoting variation within patches. So far, almost all theory has studied these two processes in isolation. Here, we use mathematical modeling to investigate how resource variation within and between habitats influences the evolution of variation in a consumer population where individuals compete in finite patches connected by dispersal. We find that locally and spatially disruptive selection typically act in concert, favoring polymorphism under a wider range of conditions than when in isolation. But when patches are small and dispersal between them is low, kin competition inhibits the emergence of polymorphism, especially when the latter is driven by local competition for resources. We further use our model to clarify what comparisons between trait and neutral genetic differentiation (Q ST / F ST comparisons) can tell about the nature of selection. Overall, our results help us understand the interaction between two major drivers of polymorphism: locally and spatially disruptive selection, and how this interaction is modulated by the unavoidable effects of kin selection under limited dispersal.
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2
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Poore HA, Stuart YE, Rennison DJ, Roesti M, Hendry AP, Bolnick DI, Peichel CL. Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution 2023; 77:110-122. [PMID: 36622692 DOI: 10.1093/evolut/qpac025] [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: 06/10/2022] [Revised: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 01/10/2023]
Abstract
Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.
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Affiliation(s)
- Hilary A Poore
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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3
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Roesti M, Groh JS, Blain SA, Huss M, Rassias P, Bolnick DI, Stuart YE, Peichel CL, Schluter D. Species divergence under competition and shared predation. Ecol Lett 2023; 26:111-123. [PMID: 36450600 DOI: 10.1111/ele.14138] [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: 07/18/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Species competing for resources also commonly share predators. While competition often drives divergence between species, the effects of shared predation are less understood. Theoretically, competing prey species could either diverge or evolve in the same direction under shared predation depending on the strength and symmetry of their interactions. We took an empirical approach to this question, comparing antipredator and trophic phenotypes between sympatric and allopatric populations of threespine stickleback and prickly sculpin fish that all live in the presence of a trout predator. We found divergence in antipredator traits between the species: in sympatry, antipredator adaptations were relatively increased in stickleback but decreased in sculpin. Shifts in feeding morphology, diet and habitat use were also divergent but driven primarily by stickleback evolution. Our results suggest that asymmetric ecological character displacement indirectly made stickleback more and sculpin less vulnerable to shared predation, driving divergence of antipredator traits between sympatric species.
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Affiliation(s)
- Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey S Groh
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Stephanie A Blain
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Magnus Huss
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Aquatic Resources, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Peter Rassias
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Yoel E Stuart
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Dolph Schluter
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Kisekelwa T, Snoeks J, Decru E, Schedel FBD, Isumbisho M, Vreven E. A mismatch between morphological and molecular data in lineages of Enteromius (Cypriniformes: Cyprinidae) from the Lowa basin (East Democratic Republic of the Congo: DRC) with the description of a new species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2135630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tchalondawa Kisekelwa
- Centre of Research in Biodiversity, Ecology, Evolution and Conservation (CRBEC), DRC
- Département de Biologie-Chimie, Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée, Institut Supérieur Pédagogique (ISP) of Bukavu, Bukavu, 854, DRC
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Jos Snoeks
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Eva Decru
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Frederic B. D. Schedel
- Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Großhaderner Straße 2, Planegg-Martinsried, 82152, Germany
| | - Mwapu Isumbisho
- Département de Biologie-Chimie, Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée, Institut Supérieur Pédagogique (ISP) of Bukavu, Bukavu, 854, DRC
| | - Emmanuel Vreven
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
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5
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Felmy A, Reznick DN, Travis J, Potter T, Coulson T. Life histories as mosaics: plastic and genetic components differ among traits that underpin life-history strategies. Evolution 2022; 76:585-604. [PMID: 35084046 PMCID: PMC9303950 DOI: 10.1111/evo.14440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Life‐history phenotypes emerge from clusters of traits that are the product of genes and phenotypic plasticity. If the impact of the environment differs substantially between traits, then life histories might not evolve as a cohesive whole. We quantified the sensitivity of components of the life history to food availability, a key environmental difference in the habitat occupied by contrasting ecotypes, for 36 traits in fast‐ and slow‐reproducing Trinidadian guppies. Our dataset included six putatively independent origins of the slow‐reproducing, derived ecotype. Traits varied substantially in plastic and genetic control. Twelve traits were influenced only by food availability (body lengths, body weights), five only by genetic differentiation (interbirth intervals, offspring sizes), 10 by both (litter sizes, reproductive timing), and nine by neither (fat contents, reproductive allotment). Ecotype‐by‐food interactions were negligible. The response to low food was aligned with the genetic difference between high‐ and low‐food environments, suggesting that plasticity was adaptive. The heterogeneity among traits in environmental sensitivity and genetic differentiation reveals that the components of the life history may not evolve in concert. Ecotypes may instead represent mosaics of trait groups that differ in their rate of evolution.
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Affiliation(s)
- Anja Felmy
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, United Kingdom
| | - David N Reznick
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California, 922521, USA
| | - Joseph Travis
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306, USA
| | - Tomos Potter
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, United Kingdom
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, United Kingdom
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6
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James ME, Arenas-Castro H, Groh JS, Allen SL, Engelstädter J, Ortiz-Barrientos D. Highly Replicated Evolution of Parapatric Ecotypes. Mol Biol Evol 2021; 38:4805-4821. [PMID: 34254128 PMCID: PMC8557401 DOI: 10.1093/molbev/msab207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origins of ecotypes are often inferred based on a phylogeny that clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic because gene flow and incomplete lineage sorting can uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography and show that this is unlikely due to gene flow between parapatric ecotypes, which was surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Henry Arenas-Castro
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Scott L Allen
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
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7
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Ishikawa A, Stuart YE, Bolnick DI, Kitano J. Copy number variation of a fatty acid desaturase gene Fads2 associated with ecological divergence in freshwater stickleback populations. Biol Lett 2021; 17:20210204. [PMID: 34428959 DOI: 10.1098/rsbl.2021.0204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fitness of aquatic animals can be limited by the scarcity of nutrients such as long-chain polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). DHA availability from diet varies among aquatic habitats, imposing different selective pressures on resident animals to optimize DHA acquisition and synthesis. For example, DHA is generally poor in freshwater ecosystems compared to marine ecosystems. Our previous work revealed that, relative to marine fishes, several freshwater fishes evolved higher copy numbers of the fatty acid desaturase2 (Fads2) gene, which encodes essential enzymes for DHA biosynthesis, likely compensating for the limited availability of DHA in freshwater. Here, we demonstrate that Fads2 copy number also varies between freshwater sticklebacks inhabiting lakes and streams with stream fish having higher Fads2 copy number. Additionally, populations with benthic-like morphology possessed higher Fads2 copy number than those with planktivore-like morphology. This may be because benthic-like fish mainly feed on DHA-deficient prey such as macroinvertebrates whereas planktivore-like fish forage more regularly on DHA-rich prey, like copepods. Our results suggest that Fads2 copy number variation arises from ecological divergence not only between organisms exploiting marine and freshwater habitats but also between freshwater organisms exploiting divergent resources.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yoel E Stuart
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan
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8
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Sowersby W, Cerca J, Wong BBM, Lehtonen TK, Chapple DG, Leal-Cardín M, Barluenga M, Ravinet M. Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation. Mol Ecol 2021; 30:5551-5571. [PMID: 34418206 DOI: 10.1111/mec.16139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/30/2022]
Abstract
Adaptive radiations have proven important for understanding the mechanisms and processes underlying biological diversity. The convergence of form and function, as well as admixture and adaptive introgression, are common in adaptive radiations. However, distinguishing between these two scenarios remains a challenge for evolutionary research. The Midas cichlid species complex (Amphilophus spp.) is a prime example of adaptive radiation, with phenotypic diversification occurring at various stages of genetic differentiation. One species, A. labiatus, has large fleshy lips, is associated with rocky lake substrates, and occurs patchily within Lakes Nicaragua and Managua. By contrast, the similar, but thin-lipped, congener, A. citrinellus, is more common and widespread. We investigated the evolutionary history of the large-lipped form, specifically regarding whether the trait has evolved independently in both lakes from ancestral thin-lipped populations, or via dispersal and/or admixture events. We collected samples from distinct locations in both lakes, and assessed differences in morphology and ecology. Using RAD-seq, we genotyped thousands of SNPs to measure population structure and divergence, demographic history, and admixture. We found significant between-species differences in ecology and morphology, local intraspecific differences in body shape and trophic traits, but only limited intraspecific variation in lip shape. Despite clear ecological differences, our genomic approach uncovered pervasive admixture between the species and low genomic differentiation, with species within lakes being genetically more similar than species between lakes. Taken together, our results suggest a single origin of large-lips, followed by pervasive admixture and adaptive introgression, with morphology being driven by local ecological opportunities, despite ongoing gene-flow.
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Affiliation(s)
- Will Sowersby
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Department of Biology, Osaka City University, Osaka, Japan
| | - José Cerca
- Frontiers of Evolutionary Zoology Research Group, Natural History Museum, University of Oslo, Oslo, Norway.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Topi K Lehtonen
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Department of Biology, University of Turku, Turku, Finland.,Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - David G Chapple
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mariana Leal-Cardín
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.,Universidad de Alcalá de Henares, Madrid, Spain
| | - Marta Barluenga
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,School of Life Sciences, University of Nottingham, Nottingham, UK
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9
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Haenel Q, Oke KB, Laurentino TG, Hendry AP, Berner D. Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish. Nat Commun 2021; 12:4850. [PMID: 34381033 PMCID: PMC8358029 DOI: 10.1038/s41467-021-25039-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/20/2021] [Indexed: 11/29/2022] Open
Abstract
How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.
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Affiliation(s)
- Quiterie Haenel
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
| | - Krista B Oke
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, AK, USA
- Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada
| | - Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
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10
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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11
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Magalhaes IS, Whiting JR, D'Agostino D, Hohenlohe PA, Mahmud M, Bell MA, Skúlason S, MacColl ADC. Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations. Nat Ecol Evol 2021; 5:251-261. [PMID: 33257817 PMCID: PMC7858233 DOI: 10.1038/s41559-020-01341-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 10/05/2020] [Indexed: 12/22/2022]
Abstract
Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.
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Affiliation(s)
- Isabel S Magalhaes
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Department of Life Sciences, Whitelands College, University of Roehampton, London, UK.
| | - James R Whiting
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, London, UK.
| | - Daniele D'Agostino
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Muayad Mahmud
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
- Erbil Polytechnic University, Kurdistan Region, Iraq
| | - Michael A Bell
- Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
- Icelandic Museum of Natural History, Suðurlandsbraut, Reykjavík, Iceland
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
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12
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Oliveira DR, Reid BN, Fitzpatrick SW. Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter ( Etheostoma caeruleum). Evol Appl 2021; 14:498-512. [PMID: 33664790 PMCID: PMC7896715 DOI: 10.1111/eva.13135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/22/2022] Open
Abstract
Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.
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Affiliation(s)
| | - Brendan N. Reid
- W.K. Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
| | - Sarah W. Fitzpatrick
- W.K. Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
- Department of Integrative BiologyMichigan State UniversityEast LansingMIUSA
- Ecology, Evolution, and Behavior ProgramMichigan State UniversityEast LansingMIUSA
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13
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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14
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Elliott Smith EA, Harrod C, Docmac F, Newsome SD. Intraspecific variation and energy channel coupling within a Chilean kelp forest. Ecology 2021; 102:e03198. [PMID: 33009678 DOI: 10.1002/ecy.3198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/10/2020] [Accepted: 08/07/2020] [Indexed: 12/21/2022]
Abstract
The widespread importance of variable types of primary production, or energy channels, to consumer communities has become increasingly apparent. However, the mechanisms underlying this "multichannel" feeding remain poorly understood, especially for aquatic ecosystems that pose unique logistical constraints given the diversity of potential energy channels. Here, we use bulk tissue isotopic analysis along with carbon isotope (δ13 C) analysis of individual amino acids to characterize the relative contribution of pelagic and benthic energy sources to a kelp forest consumer community in northern Chile. We measured bulk tissue δ13 C and δ15 N for >120 samples; of these we analyzed δ13 C values of six essential amino acids (EAA) from nine primary producer groups (n = 41) and 11 representative nearshore consumer taxa (n = 56). Using EAA δ13 C data, we employed linear discriminant analysis (LDA) to assess how distinct EAA δ13 C values were between local pelagic (phytoplankton/particulate organic matter), and benthic (kelps, red algae, and green algae) endmembers. With this model, we were able to correctly classify nearly 90% of producer samples to their original groupings, a significant improvement on traditional bulk isotopic analysis. With this EAA isotopic library, we then generated probability distributions for the most important sources of production for each individual consumer and species using a bootstrap-resampling LDA approach. We found evidence for multichannel feeding within the community at the species level. Invertebrates tended to focus on either pelagic or benthic energy, deriving 13-67% of their EAA from pelagic sources. In contrast, mobile (fish) taxa at higher trophic levels used more equal proportions of each channel, ranging from 19% to 47% pelagically derived energy. Within a taxon, multichannel feeding was a result of specialization among individuals in energy channel usage, with 37 of 56 individual consumers estimated to derive >80% of their EAA from a single channel. Our study reveals how a cutting-edge isotopic technique can characterize the dynamics of energy flow in coastal food webs, a topic that has historically been difficult to address. More broadly, our work provides a mechanism as to how multichannel feeding may occur in nearshore communities, and we suggest this pattern be investigated in additional ecosystems.
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Affiliation(s)
- Emma A Elliott Smith
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, D.C., 20560, USA
- Department of Biology, University of New Mexico, 219 Yale Blvd NE, Albuquerque, New Mexico, 87131-0001, USA
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
- Universidad de Antofagasta Stable Isotope Facility (UASIF), Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
- Núcleo Milenio Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Felipe Docmac
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
- Universidad de Antofagasta Stable Isotope Facility (UASIF), Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Seth D Newsome
- Department of Biology, University of New Mexico, 219 Yale Blvd NE, Albuquerque, New Mexico, 87131-0001, USA
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15
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Jackson JA, Friberg IM, Hablützel PI, Masud N, Stewart A, Synnott R, Cable J. Partitioning the environmental drivers of immunocompetence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141152. [PMID: 32799018 DOI: 10.1016/j.scitotenv.2020.141152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/08/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
By determining susceptibility to disease, environment-driven variation in immune responses can affect the health, productivity and fitness of vertebrates. Yet how the different components of the total environment control this immune variation is remarkably poorly understood. Here, through combining field observation, experimentation and modelling, we are able to quantitatively partition the key environmental drivers of constitutive immune allocation in a model wild vertebrate (three-spined stickleback, Gasterosteus aculeatus). We demonstrate that, in natural populations, thermal conditions and diet alone are sufficient (and necessary) to explain a dominant (seasonal) axis of variation in immune allocation. This dominant axis contributes to both infection resistance and tolerance and, in turn, to the vital rates of infectious agents and the progression of the disease they cause. Our results illuminate the environmental regulation of vertebrate immunity (given the evolutionary conservation of the molecular pathways involved) and they identify mechanisms through which immunocompetence and host-parasite dynamics might be impacted by changing environments. In particular, we predict a dominant sensitivity of immunocompetence and immunocompetence-driven host-pathogen dynamics to host diet shifts.
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Affiliation(s)
- Joseph A Jackson
- Ecoimmunology Laboratory, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Ida M Friberg
- Ecoimmunology Laboratory, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Pascal I Hablützel
- IBERS, Aberystwyth University, Aberystwyth, UK; Flanders Marine Institute, Oostende, Belgium; Laboratory of Biodiversity and Evolutionary Genomics, Biology Department, University of Leuven, Leuven, Belgium
| | - Numair Masud
- School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Rebecca Synnott
- Ecoimmunology Laboratory, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Joanne Cable
- School of Biosciences, Cardiff University, Cardiff, UK
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16
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Haines GE, Stuart YE, Hanson D, Tasneem T, Bolnick DI, Larsson HCE, Hendry AP. Adding the third dimension to studies of parallel evolution of morphology and function: An exploration based on parapatric lake-stream stickleback. Ecol Evol 2020; 10:13297-13311. [PMID: 33304538 PMCID: PMC7713967 DOI: 10.1002/ece3.6929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/04/2022] Open
Abstract
Recent methodological advances have led to a rapid expansion of evolutionary studies employing three-dimensional landmark-based geometric morphometrics (GM). GM methods generally enable researchers to capture and compare complex shape phenotypes, and to quantify their relationship to environmental gradients. However, some recent studies have shown that the common, inexpensive, and relatively rapid two-dimensional GM methods can distort important information and produce misleading results because they cannot capture variation in the depth (Z) dimension. We use micro-CT scanned threespine stickleback (Gasterosteus aculeatus Linnaeus, 1758) from six parapatric lake-stream populations on Vancouver Island, British Columbia, to test whether the loss of the depth dimension in 2D GM studies results in misleading interpretations of parallel evolution. Using joint locations described with 2D or 3D landmarks, we compare results from separate 2D and 3D shape spaces, from a combined 2D-3D shape space, and from estimates of biomechanical function. We show that, although shape is distorted enough in 2D projections to strongly influence the interpretation of morphological parallelism, estimates of biomechanical function are relatively robust to the loss of the Z dimension.
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Affiliation(s)
- Grant E. Haines
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | | | - Dieta Hanson
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | - Tania Tasneem
- Kealing Middle SchoolAustin Independent School DistrictAustinTXUSA
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Hans C. E. Larsson
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
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17
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Laurentino TG, Moser D, Roesti M, Ammann M, Frey A, Ronco F, Kueng B, Berner D. Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish. Nat Commun 2020; 11:1928. [PMID: 32317640 PMCID: PMC7174299 DOI: 10.1038/s41467-020-15657-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/19/2020] [Indexed: 11/29/2022] Open
Abstract
How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use pooled whole-genome sequence data from the original populations to identify hundreds of candidate genome regions likely under divergent selection between these habitats. Next, we generate F2 hybrids from the same lake-stream population pair in the laboratory and release thousands of juveniles into a natural stream habitat. Comparing the individuals surviving one year of stream selection to a reference sample of F2 hybrids allows us to detect frequency shifts across the candidate regions toward the genetic variants typical of the stream population-an experimental outcome consistent with polygenic directional selection. Our study reveals that adaptation in nature can be detected as a genome-wide signal over just a single generation.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Dario Moser
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Matthias Ammann
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Anja Frey
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Benjamin Kueng
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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18
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Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH, Chain FJJ. Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes. Genome Biol Evol 2020; 11:2344-2359. [PMID: 31298693 PMCID: PMC6735750 DOI: 10.1093/gbe/evz148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfälische Wilhelms University, Münster, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, USA
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19
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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20
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Geladi I, De León LF, Torchin ME, Hendry AP, González R, Sharpe DM. 100-year time series reveal little morphological change following impoundment and predator invasion in two Neotropical characids. Evol Appl 2019; 12:1385-1401. [PMID: 31417622 PMCID: PMC6691216 DOI: 10.1111/eva.12763] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/22/2018] [Indexed: 01/05/2023] Open
Abstract
Human activities are dramatically altering ecosystems worldwide, often resulting in shifts in selection regimes. In response, natural populations sometimes undergo rapid phenotypic changes, which, if adaptive, can increase their probability of persistence. However, in many instances, populations fail to undergo any phenotypic change, which might indicate a variety of possibilities, including maladaptation. In freshwater ecosystems, the impoundment of rivers and the introduction of exotic species are among the leading threats to native fishes. We examined how the construction of the Panama Canal, which formed Lake Gatun, and the subsequent invasion of the predatory Cichla monoculus influenced the morphology of two native fishes: Astyanax ruberrimus and Roeboides spp. Using a 100-year time series, we studied variation in overall body shape over time (before vs. after impoundment and invasion) as well as across space (between an invaded and an uninvaded reservoir). In addition, we examined variation in linear morphological traits associated with swim performance and predator detection/avoidance. Notwithstanding a few significant changes in particular traits in particular comparisons, we found only limited evidence for morphological change associated with these two stressors. Most observed changes were subtle, and tended to be site- and species-specific. The lack of a strong morphological response to these stressors, coupled with dramatic population declines in both species, suggests they may be maladapted to the anthropogenically perturbed environment of Lake Gatun, but direct measures of fitness would be needed to test this. In general, our results suggest that morphological responses to anthropogenic disturbances can be very limited and, when they do occur, are often complex and context-dependent.
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Affiliation(s)
- Ilke Geladi
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Luis Fernando De León
- Department of BiologyUniversity of Massachusetts BostonBostonMassachusetts
- Centro de Biodiversidad y Descubrimiento de DrogasInstituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT‐AIP)PanamaRepublic of Panama
| | - Mark E. Torchin
- Smithsonian Tropical Research InstituteBalboa, Ancon, PanamaRepublic of Panama
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Rigoberto González
- Smithsonian Tropical Research InstituteBalboa, Ancon, PanamaRepublic of Panama
| | - Diana M.T. Sharpe
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
- Smithsonian Tropical Research InstituteBalboa, Ancon, PanamaRepublic of Panama
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21
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Rennison DJ, Stuart YE, Bolnick DI, Peichel CL. Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180241. [PMID: 31154970 PMCID: PMC6560272 DOI: 10.1098/rstb.2018.0241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/24/2022] Open
Abstract
The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish ( Gasterosteus aculeatus) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake-stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake-stream stickleback, but that additional ecological factors are also important. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Diana J. Rennison
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yoel E. Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel I. Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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22
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Andres KJ, Chien H, Knouft JH. Hydrology induces intraspecific variation in freshwater fish morphology under contemporary and future climate scenarios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:421-430. [PMID: 30933798 DOI: 10.1016/j.scitotenv.2019.03.292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
Predicting future changes in habitat-associated species traits is an important step in understanding the ecological and evolutionary consequences of environmental change. However, models projecting phenotypic responses to future climate change typically assume populations will respond similarly across the range of a species, while local adaptation and spatial variation in environmental changes are rarely considered. In this study, among-population phenotypic variability was coupled with geographic variation in anticipated hydrologic changes to examine patterns of population-level phenotypic changes expected under future climatic change. To estimate phenotypic responses to watershed hydrology, phenotype-environment associations between body shape and contemporary streamflow were quantified among populations of six species of fishes (Cyprinidae). Future streamflow estimates (2070-2099) were then used to project body shapes within populations, assuming the same phenotype-environment relationships. All species exhibited significant associations between body shape and contemporary streamflow discharge and variability. However, these relationships were not consistent, even among species occupying similar vertical positions in the water column. When these phenotype-environment relationships were projected into future streamflow conditions, populations are not expected to respond uniformly across the species' ranges, and all but one species exhibited projected morphologies outside of the current range of morphological variation. These findings suggest local adaptation and spatial heterogeneity in environmental changes interact to influence variation in the degree of expected phenotypic responses to climate change at both the species and population level.
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Affiliation(s)
- Kara J Andres
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA.
| | - Huicheng Chien
- Department of Geography, SUNY New Paltz, New Paltz, NY 12561, USA
| | - Jason H Knouft
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
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23
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Henry CS, Taylor KL, Johnson JB. A new lacewing species of the Chrysoperla carnea species-group from central Asia associated with conifers (Neuroptera: Chrysopidae). J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1644385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Charles S. Henry
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Katherine L. Taylor
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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24
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Hohenlohe PA, Magalhaes IS. The Population Genomics of Parallel Adaptation: Lessons from Threespine Stickleback. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_67] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Morris MRJ, Bowles E, Allen BE, Jamniczky HA, Rogers SM. Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback. BMC Evol Biol 2018; 18:113. [PMID: 30021523 PMCID: PMC6052716 DOI: 10.1186/s12862-018-1228-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/03/2018] [Indexed: 11/25/2022] Open
Abstract
Background Populations that have repeatedly colonized novel environments are useful for studying the role of ecology in adaptive divergence – particularly if some individuals persist in the ancestral habitat. Such “contemporary ancestors” can be used to demonstrate the effects of selection by comparing phenotypic and genetic divergence between the derived population and their extant ancestors. However, evolution and demography in these “contemporary ancestors” can complicate inferences about the source (standing genetic variation, de novo mutation) and pace of adaptive divergence. Marine threespine stickleback (Gasterosteus aculeatus) have colonized freshwater environments along the Pacific coast of North America, but have also persisted in the marine environment. To what extent are marine stickleback good proxies of the ancestral condition? Results We sequenced > 5800 variant loci in over 250 marine stickleback from eight locations extending from Alaska to California, and phenotyped them for platedness and body shape. Pairwise FST varied from 0.02 to 0.18. Stickleback were divided into five genetic clusters, with a single cluster comprising stickleback from Washington to Alaska. Plate number, Eda, body shape, and candidate loci showed evidence of being under selection in the marine environment. Comparisons to a freshwater population demonstrated that candidate loci for freshwater adaptation varied depending on the choice of marine populations. Conclusions Marine stickleback are structured into phenotypically and genetically distinct populations that have been evolving as freshwater stickleback evolved. This variation complicates their usefulness as proxies of the ancestors of freshwater populations. Lessons from stickleback may be applied to other “contemporary ancestor”-derived population studies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1228-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew R J Morris
- Department of Biology, Ambrose University, 150 Ambrose Circle SW, Calgary, AB, T3H 0L5, Canada.
| | - Ella Bowles
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Brandon E Allen
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Heather A Jamniczky
- McCaig Institute for Bone and Joint Health, Department of Cell Biology & Anatomy, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4Z6, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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Runemark A, Fernández LP, Eroukhmanoff F, Sætre GP. Genomic Contingencies and the Potential for Local Adaptation in a Hybrid Species. Am Nat 2018; 192:10-22. [DOI: 10.1086/697563] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Berner D, Roesti M. Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate. Mol Ecol 2017; 26:6351-6369. [PMID: 28994152 DOI: 10.1111/mec.14373] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Genetic differentiation between divergent populations is often greater in chromosome centres than peripheries. Commonly overlooked, this broadscale differentiation pattern is sometimes ascribed to heterogeneity in crossover rate and hence linked selection within chromosomes, but the underlying mechanisms remain incompletely understood. A literature survey across 46 organisms reveals that most eukaryotes indeed exhibit a reduced crossover rate in chromosome centres relative to the peripheries. Using simulations of populations diverging into ecologically different habitats through sorting of standing genetic variation, we demonstrate that such chromosome-scale heterogeneity in crossover rate, combined with polygenic divergent selection, causes stronger hitchhiking and especially barriers to gene flow across chromosome centres. Without requiring selection on new mutations, this rapidly leads to elevated population differentiation in the low-crossover centres relative to the high-crossover peripheries of chromosomes ("Chromosome Centre-Biased Differentiation", CCBD). Using simulated and empirical data, we then show that strong CCBD between populations can provide evidence of polygenic adaptive divergence with a phase of gene flow. We further demonstrate that chromosome-scale heterogeneity in crossover rate impacts analyses beyond that of population differentiation, including the inference of phylogenies and parallel adaptive evolution among populations, the detection of genetic loci under selection, and the interpretation of the strength of selection on genomic regions. Overall, our results call for a greater appreciation of chromosome-scale heterogeneity in crossover rate in evolutionary genomics.
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Affiliation(s)
- Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Marius Roesti
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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Hanson D, Hu J, Hendry AP, Barrett RDH. Heritable gene expression differences between lake and stream stickleback include both parallel and antiparallel components. Heredity (Edinb) 2017; 119:339-348. [PMID: 28832577 PMCID: PMC5637370 DOI: 10.1038/hdy.2017.50] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/05/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
The repeated phenotypic patterns that characterize populations undergoing parallel evolution provide support for a deterministic role of adaptation by natural selection. Determining the level of parallelism also at the genetic level is thus central to our understanding of how natural selection works. Many studies have looked for repeated genomic patterns in natural populations, but work on gene expression is less common. The studies that have examined gene expression have found some support for parallelism, but those studies almost always used samples collected from the wild that potentially confounds the effects of plasticity with heritable differences. Here we use two independent pairs of lake and stream threespine stickleback (Gasterosteus aculeatus) raised in common garden conditions to assess both parallel and antiparallel (that is, similar versus different directions of lake–stream expression divergence in the two watersheds) heritable gene expression differences as measured by total RNA sequencing. We find that more genes than expected by chance show either parallel (22 genes, 0.18% of expressed genes) or antiparallel (24 genes, 0.20% of expressed genes) lake–stream expression differences. These results correspond well with previous genomic studies in stickleback ecotype pairs that found similar levels of parallelism. We suggest that parallelism might be similarly constrained at the genomic and transcriptomic levels.
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Affiliation(s)
- D Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - A P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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29
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Andreou D, Eizaguirre C, Boehm T, Milinski M. Mate choice in sticklebacks reveals that immunogenes can drive ecological speciation. Behav Ecol 2017; 28:953-961. [PMID: 29622924 PMCID: PMC5873247 DOI: 10.1093/beheco/arx074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/27/2017] [Accepted: 05/08/2017] [Indexed: 11/14/2022] Open
Abstract
Adaptation to ecologically contrasting niches can lead to the formation of new species. Theoretically, this process of ecological speciation can be driven by pleiotropic "magic traits" that genetically link natural and sexual selection. To qualify as a true magic trait, the pleiotropic function of a gene must be reflected in biologically relevant mechanisms underlying both local adaptation and mate choice. The immune genes of the major histocompatibility complex (MHC) contribute to parasite resistance and also play a major role in sexual selection. Hence, the MHC may encode a candidate magic trait. Using diverging 3-spined stickleback populations from a connected lake-river habitat, we show with mate choice experiments in a flow channel that polymorphic MHC genes probably underlie assortative mating with respect to particular habitat-adapted ecotypes, potentially resulting in reproductive isolation. By manipulating olfactory cues in controlled experiments, we show that female sticklebacks employ MHC-dependent male olfactory signals to select mates with which they can achieve a habitat-specific MHC gene structure that optimally protects their offspring against local parasites. By using MHC-based olfactory signals, females thus select individuals of their own population as mates. Our results demonstrate how mate choice and parasite resistance may be functionally linked. These findings suggest that MHC genes are pleiotropic and encode a true magic trait of biologically significant effect.
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Affiliation(s)
- Demetra Andreou
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August- Thienemann- Str. 2, D-24306, Ploen, Germany
- Department of Life and Environmental Science, Faculty of Science and Technology, Talbot Campus, Poole, BH12 5BB, UK
| | - Christophe Eizaguirre
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August- Thienemann- Str. 2, D-24306, Ploen, Germany
- GEOMAR| Helmholtz Centre for Ocean Research, Department of Evolutionary Ecology of Marine Fishes, D-24105, Kiel, Germany
- Present address: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK, and
| | - Thomas Boehm
- Max Planck Institute of Immunobiology and Epigenetics, Department of Developmental Immunology, Stuebeweg 51, D-79108 Freiburg, Germany
| | - Manfred Milinski
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August- Thienemann- Str. 2, D-24306, Ploen, Germany
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30
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Oke KB, Rolshausen G, LeBlond C, Hendry AP. How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes. Am Nat 2017; 190:1-16. [DOI: 10.1086/691989] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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Differences can hold populations together. Nature 2017; 546:218-219. [DOI: 10.1038/nature22502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Stuart YE, Veen T, Weber JN, Hanson D, Ravinet M, Lohman BK, Thompson CJ, Tasneem T, Doggett A, Izen R, Ahmed N, Barrett RDH, Hendry AP, Peichel CL, Bolnick DI. Contrasting effects of environment and genetics generate a continuum of parallel evolution. Nat Ecol Evol 2017; 1:158. [DOI: 10.1038/s41559-017-0158] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
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33
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Langerhans RB. Predictability and Parallelism of Multitrait Adaptation. J Hered 2017; 109:59-70. [DOI: 10.1093/jhered/esx043] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 05/01/2017] [Indexed: 02/03/2023] Open
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34
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Berner D, Ammann M, Spencer E, Rüegg A, Lüscher D, Moser D. Sexual isolation promotes divergence between parapatric lake and stream stickleback. J Evol Biol 2016; 30:401-411. [PMID: 27862535 DOI: 10.1111/jeb.13016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 12/26/2022]
Abstract
Speciation can be initiated by adaptive divergence between populations in ecologically different habitats, but how sexually based reproductive barriers contribute to this process is less well understood. We here test for sexual isolation between ecotypes of threespine stickleback fish residing in adjacent lake and stream habitats in the Lake Constance basin, Central Europe. Mating trials exposing females to pairings of territorial lake and stream males in outdoor mesocosms allowing for natural reproductive behaviour reveal that mating occurs preferentially between partners of the same ecotype. Compared to random mating, this sexual barrier reduces gene flow between the ecotypes by some 36%. This relatively modest strength of sexual isolation is surprising because comparing the males between the two ecotypes shows striking differentiation in traits generally considered relevant to reproductive behaviour (body size, breeding coloration, nest size). Analysing size differences among the individuals in the mating trials further indicates that assortative mating is not related to ecotype differences in body size. Overall, we demonstrate that sexually based reproductive isolation promotes divergence in lake-stream stickleback along with other known reproductive barriers, but we also caution against inferring strong sexual isolation from the observation of strong population divergence in sexually relevant traits.
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Affiliation(s)
- D Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - M Ammann
- Zoological Institute, University of Basel, Basel, Switzerland
| | - E Spencer
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - A Rüegg
- Zoological Institute, University of Basel, Basel, Switzerland
| | - D Lüscher
- Zoological Institute, University of Basel, Basel, Switzerland
| | - D Moser
- Zoological Institute, University of Basel, Basel, Switzerland
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35
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Weber JN, Bradburd GS, Stuart YE, Stutz WE, Bolnick DI. Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback. Evolution 2016; 71:342-356. [DOI: 10.1111/evo.13110] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/15/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Jesse N. Weber
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
- Division of Biological Sciences University of Montana Missoula Montana 59801
| | - Gideon S. Bradburd
- Department of Integrative Biology Michigan State University East Lansing Michigan 48824
| | - Yoel E. Stuart
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
| | - William E. Stutz
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder Boulder Colorado 80309
| | - Daniel I. Bolnick
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
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36
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Hanson D, Moore JS, Taylor EB, Barrett RDH, Hendry AP. Assessing reproductive isolation using a contact zone between parapatric lake-stream stickleback ecotypes. J Evol Biol 2016; 29:2491-2501. [PMID: 27633750 DOI: 10.1111/jeb.12978] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 09/02/2016] [Indexed: 01/09/2023]
Abstract
Ecological speciation occurs when populations evolve reproductive isolation as a result of divergent natural selection. This isolation can be influenced by many potential reproductive barriers, including selection against hybrids, selection against migrants and assortative mating. How and when these barriers act and interact in nature is understood for relatively few empirical systems. We used a mark-recapture experiment in a contact zone between lake and stream three-spined sticklebacks (Gasterosteus aculeatus, Linnaeus) to evaluate the occurrence of hybrids (allowing inferences about mating isolation), the interannual survival of hybrids (allowing inferences about selection against hybrids) and the shift in lake-like vs. stream-like characteristics (allowing inferences about selection against migrants). Genetic and morphological data suggest the occurrence of hybrids and no selection against hybrids in general, a result contradictory to a number of other studies of sticklebacks. However, we did find selection against more lake-like individuals, suggesting a barrier to gene flow from the lake into the stream. Combined with previous work on this system, our results suggest that multiple (most weakly and often asymmetric) barriers must be combining to yield substantial restrictions on gene flow. This work provides evidence of a reproductive barrier in lake-stream sticklebacks and highlights the value of assessing multiple reproductive barriers in natural contexts.
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Affiliation(s)
- D Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - J-S Moore
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - E B Taylor
- Department of Zoology and Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - A P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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37
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Marques DA, Lucek K, Haesler MP, Feller AF, Meier JI, Wagner CE, Excoffier L, Seehausen O. Genomic landscape of early ecological speciation initiated by selection on nuptial colour. Mol Ecol 2016; 26:7-24. [DOI: 10.1111/mec.13774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/30/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022]
Affiliation(s)
- David Alexander Marques
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Kay Lucek
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
- University of Sheffield; Sheffield UK
| | - Marcel Philipp Haesler
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Anna Fiona Feller
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Joana Isabel Meier
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Catherine E. Wagner
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
- Department of Botany, Biodiversity Institute; University of Wyoming; Laramie WY USA
| | - Laurent Excoffier
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Swiss Institute of Bioinformatics; Lausanne Switzerland
| | - Ole Seehausen
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
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38
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Scharnweber K, Strandberg U, Marklund MHK, Eklöv P. Combining resource use assessment techniques reveals trade‐offs in trophic specialization of polymorphic perch. Ecosphere 2016. [DOI: 10.1002/ecs2.1387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Kristin Scharnweber
- Department of Ecology and Genetics, Limnology Evolutionary Biology Centre Uppsala University Norbyvägen 18d 75236 Uppsala Sweden
| | - Ursula Strandberg
- Department of Biology University of Eastern Finland Yliopistokatu 7, PO Box 111 Joensuu 80101 Finland
| | - Maria Helena Katarina Marklund
- Department of Ecology and Genetics, Limnology Evolutionary Biology Centre Uppsala University Norbyvägen 18d 75236 Uppsala Sweden
| | - Peter Eklöv
- Department of Ecology and Genetics, Limnology Evolutionary Biology Centre Uppsala University Norbyvägen 18d 75236 Uppsala Sweden
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39
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Scharsack JP, Franke F, Erin NI, Kuske A, Büscher J, Stolz H, Samonte IE, Kurtz J, Kalbe M. Effects of environmental variation on host–parasite interaction in three-spined sticklebacks (Gasterosteus aculeatus). ZOOLOGY 2016; 119:375-83. [DOI: 10.1016/j.zool.2016.05.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/22/2016] [Accepted: 05/24/2016] [Indexed: 12/01/2022]
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40
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Lucek K, Kristjánsson BK, Skúlason S, Seehausen O. Ecosystem size matters: the dimensionality of intralacustrine diversification in Icelandic stickleback is predicted by lake size. Ecol Evol 2016; 6:5256-72. [PMID: 27551381 PMCID: PMC4984502 DOI: 10.1002/ece3.2239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/10/2016] [Accepted: 05/16/2016] [Indexed: 02/03/2023] Open
Abstract
Cases of evolutionary diversification can be characterized along a continuum from weak to strong genetic and phenotypic differentiation. Several factors may facilitate or constrain the differentiation process. Comparative analyses of replicates of the same taxon at different stages of differentiation can be useful to identify these factors. We estimated the number of distinct phenotypic groups in three‐spine stickleback populations from nine lakes in Iceland and in one marine population. Using the inferred number of phenotypic groups in each lake, genetic divergence from the marine population, and physical lake and landscape variables, we tested whether ecosystem size, approximated by lake size and depth, or isolation from the ancestral marine gene pool predicts the occurrence and the extent of phenotypic and genetic diversification within lakes. We find intralacustrine phenotypic diversification to be the rule rather than the exception, occurring in all but the youngest lake population and being manifest in ecologically important phenotypic traits. Neutral genetic data further indicate nonrandom mating in four of nine studied lakes, and restricted gene flow between sympatric phenotypic groups in two. Although neither the phenotypic variation nor the number of intralacustrine phenotypic groups was associated with any of our environmental variables, the number of phenotypic traits that were differentiated was significantly positively related to lake size, and evidence for restricted gene flow between sympatric phenotypic groups was only found in the largest lakes where trait specific phenotypic differentiation was highest.
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Affiliation(s)
- Kay Lucek
- Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Baltzerstrasse 6CH-3012 Bern Switzerland; Department of Fish Ecology and Evolution EAWAG Swiss Federal Institute of Aquatic Science and Technology Center for Ecology, Evolution and Biogeochemistry CH-6047 Kastanienbaum Switzerland; Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology Hólar University College 550 Saudárkrókur Iceland
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology Hólar University College 550 Saudárkrókur Iceland
| | - Ole Seehausen
- Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Baltzerstrasse 6CH-3012 Bern Switzerland; Department of Fish Ecology and Evolution EAWAG Swiss Federal Institute of Aquatic Science and Technology Center for Ecology, Evolution and Biogeochemistry CH-6047 Kastanienbaum Switzerland
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41
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Østbye K, Harrod C, Gregersen F, Klepaker T, Schulz M, Schluter D, Vøllestad LA. The temporal window of ecological adaptation in postglacial lakes: a comparison of head morphology, trophic position and habitat use in Norwegian threespine stickleback populations. BMC Evol Biol 2016; 16:102. [PMID: 27178328 PMCID: PMC4866279 DOI: 10.1186/s12862-016-0676-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/29/2016] [Indexed: 12/02/2022] Open
Abstract
Background Studying how trophic traits and niche use are related in natural populations is important in order to understand adaptation and specialization. Here, we describe trophic trait diversity in twenty-five Norwegian freshwater threespine stickleback populations and their putative marine ancestor, and relate trait differences to postglacial lake age. By studying lakes of different ages, depths and distance to the sea we examine key environmental variables that may predict adaptation in trophic position and habitat use. We measured trophic traits including geometric landmarks that integrated variation in head shape as well as gillraker length and number. Trophic position (Tpos) and niche use (α) were estimated from stable isotopes (δ13C, δ15N). A comparison of head shape was also made with two North American benthic-limnetic species pairs. Results We found that head shape differed between marine and freshwater sticklebacks, with marine sticklebacks having more upturned mouths, smaller eyes, larger opercula and deeper heads. Size-adjusted gillraker lengths were larger in marine than in freshwater stickleback. Norwegian sticklebacks were compared on the same head shape axis as the one differentiating the benthic-limnetic North American threespine stickleback species pairs. Here, Norwegian freshwater sticklebacks with a more “limnetic head shape” had more and longer gillrakers than sticklebacks with “benthic head shape”. The “limnetic morph” was positively associated with deeper lakes. Populations differed in α (mean ± sd: 0.76 ± 0.29) and Tpos (3.47 ± 0.27), where α increased with gillraker length. Larger fish had a higher Tpos than smaller fish. Compared to the ecologically divergent stickleback species pairs and solitary lake populations in North America, Norwegian freshwater sticklebacks had similar range in Tpos and α values, but much less trait divergences. Conclusions Our results showed trait divergences between threespine stickleback in marine and freshwater environments. Freshwater populations diverged in trophic ecology and trophic traits, but trophic ecology was not related to the elapsed time in freshwater. Norwegian sticklebacks used the same niches as the ecologically divergent North American stickleback species pairs. However, as trophic trait divergences were smaller, and not strongly associated with the ecological niche, ecological adaptations along the benthic-limnetic axis were less developed in Norwegian sticklebacks.
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Affiliation(s)
- Kjartan Østbye
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P. O. Box 1066, Blindern, N-0316, Oslo, Norway.,Faculty of Applied Ecology and Agricultural Sciences, Hedmark University of Applied Science, Campus Evenstad, NO-2480, Koppang, Norway
| | - Chris Harrod
- Department of Physiological Ecology, Max Planck Institute for Limnology, Postfach 165, D-24302, Plön, Germany.,Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humbolt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | | | - Tom Klepaker
- Department of Biology, Aquatic Behavioural Ecology Research group, University of Bergen, P. O. Box 7800, N-5020, Bergen, Norway
| | | | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Leif Asbjørn Vøllestad
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P. O. Box 1066, Blindern, N-0316, Oslo, Norway.
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42
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Marques DA, Lucek K, Meier JI, Mwaiko S, Wagner CE, Excoffier L, Seehausen O. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback. PLoS Genet 2016; 12:e1005887. [PMID: 26925837 PMCID: PMC4771382 DOI: 10.1371/journal.pgen.1005887] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/29/2016] [Indexed: 01/18/2023] Open
Abstract
Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this.
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Affiliation(s)
- David A. Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- * E-mail:
| | - Kay Lucek
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Animal and Plant Science, University of Sheffield, Sheffield, United Kingdom
| | - Joana I. Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Biodiversity Institute, University of Wyoming, Wyoming, United States of America
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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Moser D, Frey A, Berner D. Fitness differences between parapatric lake and stream stickleback revealed by a field transplant. J Evol Biol 2016; 29:711-9. [PMID: 26709953 DOI: 10.1111/jeb.12817] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/16/2015] [Accepted: 12/18/2015] [Indexed: 01/18/2023]
Abstract
Molecular comparisons of populations diverging into ecologically different environments often reveal strong differentiation in localized genomic regions, with the remainder of the genome being weakly differentiated. This pattern of heterogeneous genomic divergence, however, is rarely connected to direct measurements of fitness differences among populations. We here do so by performing a field enclosure experiment in threespine stickleback fish residing in a lake and in three replicate adjoining streams, and displaying weak yet heterogeneous genomic divergence between these habitats. Tracking survival over 29 weeks, we consistently find that lake genotypes transplanted into the streams suffer greatly reduced viability relative to local stream genotypes and that the performance of F1 hybrid genotypes is intermediate. This observed selection against migrants and hybrids combines to a total reduction in gene flow from the lake into streams of around 80%. Overall, our study identifies a strong reproductive barrier between parapatric stickleback populations, and cautions against inferring weak fitness differences between populations exhibiting weak overall genomic differentiation.
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Affiliation(s)
- D Moser
- Zoological Institute, University of Basel, Basel, Switzerland
| | - A Frey
- Zoological Institute, University of Basel, Basel, Switzerland
| | - D Berner
- Zoological Institute, University of Basel, Basel, Switzerland
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44
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Oke KB, Bukhari M, Kaeuffer R, Rolshausen G, Räsänen K, Bolnick DI, Peichel CL, Hendry AP. Does plasticity enhance or dampen phenotypic parallelism? A test with three lake–stream stickleback pairs. J Evol Biol 2015; 29:126-43. [DOI: 10.1111/jeb.12767] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 12/19/2022]
Affiliation(s)
- K. B. Oke
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - M. Bukhari
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - R. Kaeuffer
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - G. Rolshausen
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - K. Räsänen
- Department of Aquatic Ecology Eawag and Institute of Integrative Biology ETH‐Zurich Duebendorf Switzerland
| | - D. I. Bolnick
- Department of Integrative Biology University of Texas at Austin Austin TX USA
| | - C. L. Peichel
- Divisions of Basic Sciences and Human Biology Fred Hutchinson Cancer Research Center Seattle WA USA
| | - A. P. Hendry
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
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45
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Hanson D, Barrett RDH, Hendry AP. Testing for parallel allochronic isolation in lake-stream stickleback. J Evol Biol 2015; 29:47-57. [DOI: 10.1111/jeb.12761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/02/2015] [Accepted: 09/10/2015] [Indexed: 01/17/2023]
Affiliation(s)
- D. Hanson
- Redpath Museum and Department of Biology; McGill University; Montreal QC Canada
| | - R. D. H. Barrett
- Redpath Museum and Department of Biology; McGill University; Montreal QC Canada
| | - A. P. Hendry
- Redpath Museum and Department of Biology; McGill University; Montreal QC Canada
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46
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Ravinet M, Westram A, Johannesson K, Butlin R, André C, Panova M. Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale. Mol Ecol 2015. [PMID: 26222268 DOI: 10.1111/mec.13332] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small 'wave' ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, 'crab' ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel, and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However, the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this, we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities amongst ecotype pairs on three close islands (<10 km distance) connected by weak gene flow (Nm ~ 0.03) and with recent common ancestry (<10 000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared amongst all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.
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Affiliation(s)
- Mark Ravinet
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden.,Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan
| | - Anja Westram
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Kerstin Johannesson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden
| | - Roger Butlin
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden
| | - Marina Panova
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden
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Rolshausen G, Muttalib S, Kaeuffer R, Oke KB, Hanson D, Hendry AP. When maladaptive gene flow does not increase selection. Evolution 2015. [DOI: 10.1111/evo.12739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Gregor Rolshausen
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Shahin Muttalib
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Renaud Kaeuffer
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Krista B. Oke
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
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48
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Karvonen A, Lucek K, Marques DA, Seehausen O. Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus). PLoS One 2015; 10:e0130579. [PMID: 26086778 PMCID: PMC4472517 DOI: 10.1371/journal.pone.0130579] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/21/2015] [Indexed: 11/18/2022] Open
Abstract
Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.
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Affiliation(s)
- Anssi Karvonen
- University of Jyväskylä, Department of Biological and Environmental Science, FI-40014 University of Jyväskylä, Jyväskylä, Finland
- * E-mail:
| | - Kay Lucek
- Eawag, Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution, Kastanienbaum, Switzerland
- Division of Aquatic Ecology & Macroevolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David A. Marques
- Eawag, Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution, Kastanienbaum, Switzerland
- Division of Aquatic Ecology & Macroevolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Eawag, Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution, Kastanienbaum, Switzerland
- Division of Aquatic Ecology & Macroevolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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49
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Lake-Stream Divergence in Stickleback Life History: A Plastic Response to Trophic Niche Differentiation? Evol Biol 2015. [DOI: 10.1007/s11692-015-9327-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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50
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Ravinet M, Hynes R, Poole R, Cross TF, McGinnity P, Harrod C, Prodöhl PA. Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks. PLoS One 2015; 10:e0122825. [PMID: 25874617 PMCID: PMC4397041 DOI: 10.1371/journal.pone.0122825] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/14/2015] [Indexed: 11/28/2022] Open
Abstract
Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L.) forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12), we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an important foundation for future work investigating the dynamics of gene flow and adaptive divergence in this newly discovered stickleback contact zone.
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Affiliation(s)
- Mark Ravinet
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Rosaleen Hynes
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Russell Poole
- Marine Institute, Furnace, Newport, County Mayo, Ireland
| | - Tom F. Cross
- Aquaculture, Fisheries and Development Centre, School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - Phil McGinnity
- Aquaculture, Fisheries and Development Centre, School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - Chris Harrod
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paulo A. Prodöhl
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- * E-mail:
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