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Boughman JW, Brand JA, Brooks RC, Bonduriansky R, Wong BBM. Sexual selection and speciation in the Anthropocene. Trends Ecol Evol 2024:S0169-5347(24)00042-9. [PMID: 38503640 DOI: 10.1016/j.tree.2024.02.005] [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: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/21/2024]
Abstract
Anthropogenic change threatens global biodiversity by causing severe ecological disturbance and extinction. Here, we consider the effects of anthropogenic change on one process that generates biodiversity. Sexual selection (a potent evolutionary force and driver of speciation) is highly sensitive to the environment and, thus, vulnerable to anthropogenic ecological change. Anthropogenic alterations to sexual display and mate preference can make it harder to distinguish between conspecific and heterospecific mates or can weaken divergence via sexual selection, leading to higher rates of hybridization and biodiversity loss. Occasionally, anthropogenically altered sexual selection can abet diversification, but this appears less likely than biodiversity loss. In our rapidly changing world, a full understanding of sexual selection and speciation requires a global change perspective.
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Affiliation(s)
- Janette W Boughman
- Department of Integrative Biology & Evolution, Ecology and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
| | - Jack A Brand
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia; Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Västerbotten, SE-907 36, Sweden
| | - Robert C Brooks
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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2
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Tiddy IC, Schneider K, Elmer KR. Environmental correlates of adaptive diversification in postglacial freshwater fishes. JOURNAL OF FISH BIOLOGY 2024; 104:517-535. [PMID: 37984834 DOI: 10.1111/jfb.15621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
Determining how environmental conditions contribute to divergence among populations and drive speciation is fundamental to resolving mechanisms and understanding outcomes in evolutionary biology. Postglacial freshwater fish species in the Northern Hemisphere are ideal biological systems to explore the effects of environment on diversification in morphology, ecology, and genetics (ecomorph divergences) within lakes. To date, various environmental factors have been implicated in the presence of multiple ecomorphs within particular lakes or regions. However, concerted evidence for generalizable patterns in environmental variables associated with speciation across geographical regions and across species and genera has been lacking. Here, we aimed to identify key biotic and abiotic factors associated with ecological divergence of postglacial freshwater fish species into multiple sympatric ecomorphs, focusing on species in the well-studied, widespread, and co-distributed genera Gasterosteus, Salvelinus, and Coregonus (stickleback, charr, and whitefish, respectively). We found that the presence of multiple sympatric ecomorphs tended to be associated with increasing lake surface area, maximum depth, and nutrient availability. In addition, predation, competition, and prey availability were suggested to play a role in divergence into multiple ecomorphs, but the effects of biotic factors require further study. Although we identified several environmental factors correlated with the presence of multiple ecomorphs, there were substantial data gaps across species and regions. An improved understanding of these systems may provide insight into both generalizable environmental factors involved in speciation in other systems, and potential ecological and evolutionary responses of species complexes when these variables are altered by environmental change.
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Affiliation(s)
- Isabelle C Tiddy
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Kevin Schneider
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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3
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Ålund M, Cenzer M, Bierne N, Boughman JW, Cerca J, Comerford MS, Culicchi A, Langerhans B, McFarlane SE, Möst MH, North H, Qvarnström A, Ravinet M, Svanbäck R, Taylor SA. Anthropogenic Change and the Process of Speciation. Cold Spring Harb Perspect Biol 2023; 15:a041455. [PMID: 37788888 PMCID: PMC10691492 DOI: 10.1101/cshperspect.a041455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.
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Affiliation(s)
- Murielle Ålund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Meredith Cenzer
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Nicolas Bierne
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier 34095, France
| | - Janette W Boughman
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | | | - Alessandro Culicchi
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Brian Langerhans
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - S Eryn McFarlane
- Department of Botany, University of Wyoming, Laramie, Wyoming 82071, USA
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Markus H Möst
- Research Department for Limnology, University of Innsbruck, Innsbruck 6020, Austria
| | - Henry North
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard Svanbäck
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
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4
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Baer J, Schliewen UK, Schedel FDB, Straube N, Roch S, Brinker A. Cryptic persistence and loss of local endemism in Lake Constance charr subject to anthropogenic disturbance. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2773. [PMID: 36317855 DOI: 10.1002/eap.2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
In the welcome circumstance that species believed extinct are rediscovered, it is often the case that biological knowledge acquired before the presumed extinction is limited. Efforts to address these knowledge gaps, in particular to assess the taxonomic integrity and conservation status of such species, can be hampered by a lack of genetic data and scarcity of samples in museum collections. Here, we present a proof-of-concept case study based on a multidisciplinary data evaluation approach to tackle such problems. The approach was developed after the rediscovery, 40 years after its presumed extinction, of the enigmatic Lake Constance deep-water charr Salvelinus profundus. Targeted surveys led to the capture of further species and additional sympatric normal charr, Salvelinus cf. umbla. Since the lake had been subject to massive stocking in the past, an evaluation of the genetic integrity of both extant forms was called for in order to assess possible introgression. A two-step genomic approach was developed based on restriction site associated DNA (RAD). Diagnostic population genomic (single nucleotide polymorphism [SNP]) data were harvested from contemporary samples and used for RNA bait design to perform target capture in DNA libraries of archival scale material, enabling a comparison between extant and historic samples. Furthermore, life history traits and morphological data for both extant forms were gathered and compared with historical data from the past 60-120 years. While extant deep-water charr matched historical deep-water specimens in body shape, gill raker count, and growth rates, significant differences were discovered between historical and extant normal charr. These resulted were supported by genomic analyses of contemporary samples, revealing the two extant forms to be highly divergent. The results of population assignment tests suggest that the endemic deep-water charr persisted in Lake Constance during the eutrophic phase, but not one of the historical genomic samples could be assigned to the extant normal charr taxon. Stocking with non-endemic charr seems to be the most likely reason for these changes. This proof-of-concept study presents a multidisciplinary data evaluation approach that simultaneously tests population genomic integrity and addresses some of the conservation issues arising from rediscovery of a species characterized by limited data availability.
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Affiliation(s)
- Jan Baer
- Fisheries Research Station Baden-Württemberg, Langenargen, Germany
| | | | - Frederic D B Schedel
- SNSB-ZSM Bavarian State Collection of Zoology, Munich, Germany
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Nicolas Straube
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - Samuel Roch
- Fisheries Research Station Baden-Württemberg, Langenargen, Germany
| | - Alexander Brinker
- Fisheries Research Station Baden-Württemberg, Langenargen, Germany
- University of Konstanz, Institute for Limnology, Constance, Germany
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5
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Selz OM, Seehausen O. A taxonomic revision of ten whitefish species from the lakes Lucerne, Sarnen, Sempach and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae). Zookeys 2023; 1144:95-169. [DOI: 10.3897/zookeys.1144.67747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/22/2022] [Indexed: 02/04/2023] Open
Abstract
The taxonomy of the endemic whitefish of the lakes of the Reuss River system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, is reviewed and revised. Lake Lucerne harbours five species. Coregonus intermundiasp. nov. and C. suspensussp. nov., are described. Coregonus nobilis Haack, 1882, C. suidteri Fatio, 1885, and C. zugensis Nüsslin, 1882, are redescribed. Genetic studies have shown that C. suidteri and C. zugensis are composed of several distinct species endemic to different lakes. The names C. suidteri and C. zugensis are restricted to the species of lakes Sempach and Zug, respectively. The whitefish populations previously referred to as C. suidteri and C. zugensis from Lake Lucerne are described as C. litoralissp. nov. and C. muellerisp. nov., respectively. Furthermore, the whitefish from Lake Zug that were previously referred to as C. suidteri are described as C. supersumsp. nov. A holotype is designated for C. supersum that was previously one of two syntypes of C. zugensis. The other syntype is retained for C. zugensis. Coregonus obliterussp. nov. is described from Lake Zug, and C. obliterus and C. zugensis from Lake Zug are extinct. Finally, we describe C. sarnensissp. nov. from lakes Sarnen and Alpnach. Coregonus suidteri from Lake Sempach shows strong signals of introgression from deliberately translocated non-native whitefish species, which questions if the extant population still carries a genetic legacy from the original species and thus may need to be considered extinct. Coregonus suspensus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance. It is therefore compared to all known and described species of Lake Constance: C. wartmanni Bloch, 1784, C. macrophthalmus Nüsslin, 1882, C. arenicolus Kottelat,1997, and C. gutturosus Gmelin, 1818.
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6
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Závorka L, Blanco A, Chaguaceda F, Cucherousset J, Killen SS, Liénart C, Mathieu-Resuge M, Němec P, Pilecky M, Scharnweber K, Twining CW, Kainz MJ. The role of vital dietary biomolecules in eco-evo-devo dynamics. Trends Ecol Evol 2023; 38:72-84. [PMID: 36182405 DOI: 10.1016/j.tree.2022.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 12/30/2022]
Abstract
The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization.
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Affiliation(s)
- Libor Závorka
- WasserCluster Lunz - Biologische Station, Inter-university Centre for Aquatic Ecosystem Research, A-3293 Lunz am See, Austria.
| | - Andreu Blanco
- Centro de Investigación Mariña, Universidade de Vigo, EcoCost, Campus de Vigo, As Lagoas, Marcosende, 36310, Vigo, Spain
| | - Fernando Chaguaceda
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Box 7050, 750 07 Uppsala, Sweden
| | - Julien Cucherousset
- Laboratoire Evolution et Diversité Biologique (UMR 5174 EDB), CNRS, Université Paul Sabatier - Toulouse III, 31062 Toulouse, France
| | - Shaun S Killen
- School of Biodiversity, One Health & Veterinary Medicine, Graham Kerr Building, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Camilla Liénart
- Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, Hanko, 10900, Finland
| | - Margaux Mathieu-Resuge
- WasserCluster Lunz - Biologische Station, Inter-university Centre for Aquatic Ecosystem Research, A-3293 Lunz am See, Austria; Université de Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, Brittany, France; UMR DECOD (Ecosystem Dynamics and Sustainability), Ifremer, INRAE, Institut Agro, Plouzané, France
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, CZ-12844 Prague, Czech Republic
| | - Matthias Pilecky
- WasserCluster Lunz - Biologische Station, Inter-university Centre for Aquatic Ecosystem Research, A-3293 Lunz am See, Austria; Danube University Krems, Dr. Karl Dorrek Straße 30, A-3500 Krems, Austria
| | - Kristin Scharnweber
- University of Potsdam, Plant Ecology and Nature Conservation, Am Mühlenberg 3, 14476 Potsdam, Germany
| | - Cornelia W Twining
- Department of Fish Ecology and Evolution, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047 Kastanienbaum, Switzerland
| | - Martin J Kainz
- WasserCluster Lunz - Biologische Station, Inter-university Centre for Aquatic Ecosystem Research, A-3293 Lunz am See, Austria; Danube University Krems, Dr. Karl Dorrek Straße 30, A-3500 Krems, Austria
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7
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Wedekind C, Vonlanthen P, de Guttry C, Stadelmann R, Stadelmann N, Pirat A, Perroud G. Persistent high hatchery recruitment despite advanced reoligotrophication and significant natural spawning in a whitefish. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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8
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Fang B, Momigliano P, Kahilainen KK, Merilä J. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 2022; 76:1905-1913. [PMID: 35797649 DOI: 10.1111/evo.14559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, 36310, Spain
| | - Kimmo K Kahilainen
- Lammi Biological Station, University of Helsinki, Lammi, 16900, Finland.,Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, 99490, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
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9
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DeWeber JT, Baer J, Rösch R, Brinker A. Turning summer into winter: nutrient dynamics, temperature, density dependence and invasive species drive bioenergetic processes and growth of a keystone coldwater fish. OIKOS 2022. [DOI: 10.1111/oik.09316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- J. Tyrell DeWeber
- Fisheries Research Station Baden‐Württemberg Langenargen Germany
- Inst. of Inland Fisheries in Potsdam‐Sacrow Potsdam Germany
| | - Jan Baer
- Fisheries Research Station Baden‐Württemberg Langenargen Germany
| | - Roland Rösch
- Fisheries Research Station Baden‐Württemberg Langenargen Germany
| | - Alexander Brinker
- Fisheries Research Station Baden‐Württemberg Langenargen Germany
- Inst. for Limnology, Univ. of Constance Konstanz Germany
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10
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Frei D, De-Kayne R, Selz OM, Seehausen O, Feulner PGD. Genomic variation from an extinct species is retained in the extant radiation following speciation reversal. Nat Ecol Evol 2022; 6:461-468. [PMID: 35210577 DOI: 10.1038/s41559-022-01665-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022]
Abstract
Ecosystem degradation and biodiversity loss are major global challenges. When reproductive isolation between species is contingent on the interaction of intrinsic lineage traits with features of the environment, environmental change can weaken reproductive isolation and result in extinction through hybridization. By this process called speciation reversal, extinct species can leave traces in genomes of extant species through introgressive hybridization. Using historical and contemporary samples, we sequenced all four species of an Alpine whitefish radiation before and after anthropogenic lake eutrophication and the associated loss of one species through speciation reversal. Despite the extinction of this taxon, substantial fractions of its genome, including regions shaped by positive selection before eutrophication, persist within surviving species as a consequence of introgressive hybridization during eutrophication. Given the prevalence of environmental change, studying speciation reversal and its genomic consequences provides fundamental insights into evolutionary processes and informs biodiversity conservation.
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Affiliation(s)
- David Frei
- Department of Fish Ecology and Evolution, Center for 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, Bern, Switzerland
| | - Rishi De-Kayne
- Department of Fish Ecology and Evolution, Center for 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, Bern, Switzerland
| | - Oliver M Selz
- Department of Fish Ecology and Evolution, Center for 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, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Center for 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, Bern, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Center for 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, Bern, Switzerland.
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11
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Crotti M, Bean CW, Gowans ARD, Winfield IJ, Butowska M, Wanzenböck J, Bondarencko G, Praebel K, Adams CE, Elmer KR. Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus). J Evol Biol 2021; 34:1954-1969. [PMID: 34653264 PMCID: PMC9251650 DOI: 10.1111/jeb.13948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022]
Abstract
Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome‐wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (FST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome‐wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto‐nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre‐glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum.
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Affiliation(s)
- Marco Crotti
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK.,NatureScot, Clydebank, UK
| | | | - Ian J Winfield
- Lake Ecosystems Group, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Magdalena Butowska
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Josef Wanzenböck
- Research Institute for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | | | - Kim Praebel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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12
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Jacobs A, Elmer KR. Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish. Mol Ecol 2021; 30:4955-4969. [PMID: 33502030 PMCID: PMC8653899 DOI: 10.1111/mec.15817] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 12/25/2022]
Abstract
Understanding the contribution of different molecular processes to evolution and development is crucial for identifying the mechanisms of adaptation. Here, we used RNA-sequencing data to test the importance of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into sympatric benthic and pelagic ecotypes across multiple independent lakes. We found that genes differentially spliced between ecotypes were mostly not differentially expressed (<6% overlap) and were involved in different biological processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were involved in metabolism, immunity and growth. Furthermore, alternative splicing and gene expression were mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7%-10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks ("hub genes") and were annotated to significantly more gene ontology terms compared to nondifferentially spliced genes, consistent with a higher level of pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary processes important for local adaptation. This provides novel insights into the importance of contrasting but putatively complementary molecular processes in rapid parallel adaptive evolution.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
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13
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Crotti M, Yohannes E, Winfield IJ, Lyle AA, Adams CE, Elmer KR. Rapid adaptation through genomic and epigenomic responses following translocations in an endangered salmonid. Evol Appl 2021; 14:2470-2489. [PMID: 34745338 PMCID: PMC8549615 DOI: 10.1111/eva.13267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying the molecular mechanisms facilitating adaptation to new environments is a key question in evolutionary biology, especially in the face of current rapid and human-induced changes. Translocations have become an important tool for species conservation, but the attendant small population sizes and new ecological pressures might affect phenotypic and genotypic variation and trajectories dramatically and in unknown ways. In Scotland, the European whitefish (Coregonus lavaretus) is native to only two lakes and vulnerable to extirpation. Six new refuge populations were established over the last 30 years as a conservation measure. In this study, we examined whether there is a predictable ecological and evolutionary response of these fishes to translocation. We found eco-morphological differences, as functional traits relating to body shape differed between source and refuge populations. Dual isotopic analyses suggested some ecological release, with the diets in refuge populations being more diverse than in source populations. Analyses of up to 9117 genome-mapped SNPs showed that refuge populations had reduced genetic diversity and elevated inbreeding and relatedness relative to source populations, though genomic differentiation was low (F ST = 0.002-0.030). We identified 14 genomic SNPs that showed shared signals of a selective response to translocations, including some located near or within genes involved in the immune system, nervous system and hepatic functions. Analysis of up to 120,897 epigenomic loci identified a component of consistent differential methylation between source and refuge populations. We found that epigenomic variation and genomic variation were associated with morphological variation, but we were not able to infer an effect of population age because the patterns were also linked with the methodology of the translocations. These results show that conservation-driven translocations affect evolutionary potential by impacting eco-morphological, genomic and epigenomic components of diversity, shedding light on acclimation and adaptation process in these contexts.
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Affiliation(s)
- Marco Crotti
- Institute of BiodiversityAnimal Health & Comparative MedicineCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - Elizabeth Yohannes
- Limnological InstituteUniversity of KonstanzKonstanzGermany
- Present address:
Max‐Planck Institute of Animal BehaviorAm Obstberg 1D‐78315RadolfzellGermany
- Present address:
University of KonstanzKonstanzGermany
| | - Ian J. Winfield
- Lake Ecosystems GroupUK Centre for Ecology & HydrologyLancaster Environment CentreBailrigg, LancasterUK
| | - Alex A. Lyle
- Scottish Centre for Ecology and the Natural EnvironmentUniversity of GlasgowRowardennanUK
| | - Colin E. Adams
- Institute of BiodiversityAnimal Health & Comparative MedicineCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- Scottish Centre for Ecology and the Natural EnvironmentUniversity of GlasgowRowardennanUK
| | - Kathryn R. Elmer
- Institute of BiodiversityAnimal Health & Comparative MedicineCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
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14
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Salmón P, Jacobs A, Ahrén D, Biard C, Dingemanse NJ, Dominoni DM, Helm B, Lundberg M, Senar JC, Sprau P, Visser ME, Isaksson C. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat Commun 2021; 12:2983. [PMID: 34016968 PMCID: PMC8137928 DOI: 10.1038/s41467-021-23027-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 04/01/2021] [Indexed: 02/03/2023] Open
Abstract
Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.
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Affiliation(s)
- Pablo Salmón
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Arne Jacobs
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Dag Ahrén
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Clotilde Biard
- grid.462350.6Sorbonne Université, UPEC, Paris 7, CNRS, INRA, IRD, Institut d’Écologie et des Sciences de l’Environnement de Paris, iEES Paris, F-75005 Paris, France
| | - Niels J. Dingemanse
- grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Davide M. Dominoni
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Barbara Helm
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK ,grid.4830.f0000 0004 0407 1981Present Address: GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Max Lundberg
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Juan Carlos Senar
- grid.507605.10000 0001 1958 5537Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | - Philipp Sprau
- grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Marcel E. Visser
- grid.418375.c0000 0001 1013 0288Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Caroline Isaksson
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
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15
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Selz OM, Dönz CJ, Vonlanthen P, Seehausen O. A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). Zookeys 2020; 989:79-162. [PMID: 33223897 PMCID: PMC7669820 DOI: 10.3897/zookeys.989.32822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: Coregonus steinmanni sp. nov., Coregonus profundus sp. nov. and Coregonus acrinasus sp. nov. are endemic to Lake Thun; Coregonus Brienzii sp. nov. is endemic to Lake Brienz; and C. alpinus, C. albellus, and C. fatioi from lakes Brienz and Thun are redescribed. One of these species, C. alpinus, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name C. alpinus is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. Coregonus acrinasus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, C. wartmanni, C. macrophthalmus, C. arenicolus, and C. gutturosus.
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Affiliation(s)
- Oliver M Selz
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland University of Bern Bern Switzerland
| | - Carmela J Dönz
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland University of Bern Bern Switzerland
| | - Pascal Vonlanthen
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquabios GmbH, Les Fermes 57, 1792 Cordast, Switzerland Aquabios GmbH Cordast Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland University of Bern Bern Switzerland
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16
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Koene JP, Elmer KR, Adams CE. Intraspecific variation and structuring of phenotype in a lake-dwelling species are driven by lake size and elevation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The fragmented, heterogeneous and relatively depauperate ecosystems of recently glaciated lakes present contrasting ecological opportunities for resident fish. Across a species, local adaptation may induce diverse and distinct phenotypic responses to various selection pressures. We tested for intraspecific phenotypic structuring by population in a common native lake-dwelling fish species across a medium-scale geographic region with considerable variation in lake types. We investigated potential lake-characteristic drivers of trophic morphology. Using geometric morphometric techniques, we quantified the head shapes of 759 adult brown trout (Salmo trutta L.) from 28 lakes and reservoirs across Scotland. Multivariate statistical analyses showed that almost all populations differed from one another. Trout from larger and deeper lakes had deeper, but shorter heads, and smaller eyes. Higher elevation lakes were associated with fish with shorter heads and jaws. Within-population shape variation also differed by population, and was positively correlated with lake surface area and depth. Trout within reservoirs differed subtly from those in natural lakes, having larger eyes, shorter jaws and greater variability. This study documents an extraordinary morphological variation between and within populations of brown trout, and demonstrates the role of the extrinsic environment in driving phenotypic structuring over a medium-scale and varied geographic area.
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Affiliation(s)
- J Peter Koene
- Scottish Centre for Ecology and the Natural Environment (SCENE), University of Glasgow, Rowardennan, Glasgow, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Colin E Adams
- Scottish Centre for Ecology and the Natural Environment (SCENE), University of Glasgow, Rowardennan, Glasgow, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
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17
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Ridgway MS, Piette‐Lauzière G, Bell AH, Turgeon J. Isotopic niche size of Coregonus artedi (sensu lato) Increases in the presence of Mysis diluviana, expanded habitat use and phenotypic diversity. Ecol Evol 2020; 10:11713-11726. [PMID: 33144995 PMCID: PMC7593162 DOI: 10.1002/ece3.6807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 02/03/2023] Open
Abstract
Post-glacial colonization of lakes in Algonquin Park, Ontario, Canada resulted in food webs with cisco (Coregonus artedi sensu lato) and either Mysis diluviana or Chaoborus spp. as the dominant diel migrator. Mysis as prey, its diel movements and benthic occupancy, are hypothesized to be key elements of ecological opportunity for cisco diversity in the Laurentian Great Lakes. If correct, the hypothesis strongly implies that lakes with Mysis would have greater trophic niche size and drive greater adaptive radiation of cisco forms relative to lakes without Mysis. The dichotomy in diel migrator in Algonquin Park lakes was an opportunity to assess the isotopic niche size of cisco (δ15N and δ13C) and determine if niche size expands with Mysis presence. We found the presence of Mysis is necessary to expand isotopic niche size in our study lakes. The use of habitats not typically associated with the ancestral form of cisco (e.g., benthic habitats) and phenotypic diversity (blackfin and cisco) also continue to expand niche size in Mysis-based food webs. Partial ecological speciation based on a large niche space appears to be present in one lake (Cauchon Lake) where use of alternative habitats is the only real difference in cisco. The presence of blackfin expands niche space in Cedar and Radiant Lakes. This was not matched in Hogan Lake where niche space was relatively smaller with similar forms. Possible reasons for this discrepancy may be related to the asymmetric basin of Hogan Lake and whether the two forms overlap during cool and cold-water periods of the annual temperature cycle. By comparing trophic niche size among lakes with and without Mysis, we conclude that Mysis provides a key ecological opportunity for cisco diversity in our study lakes and likely more widely.
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Affiliation(s)
- Mark S. Ridgway
- Harkness Laboratory of Fisheries Research, Aquatic Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughONCanada
| | | | - Allan H. Bell
- Harkness Laboratory of Fisheries Research, Aquatic Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughONCanada
| | - Julie Turgeon
- Département de biologieUniversité LavalQuébecQCCanada
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18
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Crotti M, Adams CE, Etheridge EC, Bean CW, Gowans ARD, Knudsen R, Lyle AA, Maitland PS, Winfield IJ, Elmer KR, Præbel K. Geographic hierarchical population genetic structuring in British European whitefish (Coregonus lavaretus) and its implications for conservation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01298-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe European whitefish Coregonus lavaretus complex represents one of the most diverse radiations within salmonids, with extreme morphological and genetic differentiation across its range. Such variation has led to the assignment of many populations to separate species. In Great Britain, the seven native populations of C. lavaretus (two in Scotland, four in England, one in Wales) were previously classified into three species, and recent taxonomic revision resurrected the previous nomenclature. Here we used a dataset of 15 microsatellites to: (1) investigate the genetic diversity of British populations, (2) assess the level of population structure and the relationships between British populations. Genetic diversity was highest in Welsh (HO = 0.50, AR = 5.29), intermediate in English (HO = 0.41–0.50, AR = 2.83–3.88), and lowest in Scottish populations (HO = 0.28–0.35, AR = 2.56–3.04). Population structure analyses indicated high genetic differentiation (global FST = 0.388) between all populations but for the two Scottish populations (FST = 0.063) and two English populations (FST = 0.038). Principal component analysis and molecular ANOVA revealed separation between Scottish, English, and Welsh populations, with the Scottish populations being the most diverged. We argue that the data presented here are not sufficient to support a separation of the British European whitefish populations into three separate species, but support the delineation of different ESUs for these populations.
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19
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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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20
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Chafin TK, Douglas MR, Martin BT, Douglas ME. Hybridization drives genetic erosion in sympatric desert fishes of western North America. Heredity (Edinb) 2019; 123:759-773. [PMID: 31431737 PMCID: PMC6834602 DOI: 10.1038/s41437-019-0259-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 01/26/2023] Open
Abstract
Many species have evolved or currently coexist in sympatry due to differential adaptation in a heterogeneous environment. However, anthropogenic habitat modifications can either disrupt reproductive barriers or obscure environmental conditions which underlie fitness gradients. In this study, we evaluated the potential for an anthropogenically-mediated shift in reproductive boundaries that separate two historically sympatric fish species (Gila cypha and G. robusta) endemic to the Colorado River Basin using ddRAD sequencing of 368 individuals. We first examined the integrity of reproductive isolation while in sympatry and allopatry, then characterized hybrid ancestries using genealogical assignment tests. We tested for localized erosion of reproductive isolation by comparing site-wise genomic clines against global patterns and identified a breakdown in the drainage-wide pattern of selection against interspecific heterozygotes. This, in turn, allowed for the formation of a hybrid swarm in one tributary, and asymmetric introgression where species co-occur. We also detected a weak but significant relationship between genetic purity and degree of consumptive water removal, suggesting a role for anthropogenic habitat modifications in undermining species boundaries or expanding historically limited introgression. In addition, results from basin-wide genomic clines suggested that hybrids and parental forms are adaptively nonequivalent. If so, then a failure to manage for hybridization will exacerbate the long-term extinction risk in parental populations. These results reinforce the role of anthropogenic habitat modification in promoting interspecific introgression in sympatric species by relaxing divergent selection. This, in turn, underscores a broader role for hybridization in decreasing global biodiversity within rapidly deteriorating environments.
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Affiliation(s)
- Tyler K Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Bradley T Martin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Michael E Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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