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Chavarie L, Muir AM, Zimmerman MS, Baillie SM, Hansen MJ, Nate NA, Yule DL, Middel T, Bentzen P, Krueger CC. Challenge to the model of lake charr evolution: shallow- and deep-water morphs exist within a small postglacial lake. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Louise Chavarie
- Center for Systems Integration and Sustainability; Michigan State University; 115 Manly Miles Building, 1405 South Harrison Road East Lansing Michigan USA
| | - Andrew M. Muir
- Great Lakes Fishery Commission; 2100 Commonwealth Blvd. Suite 100 Ann Arbor Michigan USA
| | - Mara S. Zimmerman
- Washington Department of Fish and Wildlife; 600 Capitol Way N. Olympia Washington USA
| | - Shauna M. Baillie
- Department of Biology; Dalhousie University; 1355 Oxford St. Halifax Nova Scotia Canada
| | - Michael J. Hansen
- United States Geological Survey; Hammond Bay Biological Station; 11188 Ray Road Millersburg Michigan USA
| | - Nancy A. Nate
- Center for Systems Integration and Sustainability; Michigan State University; 115 Manly Miles Building, 1405 South Harrison Road East Lansing Michigan USA
| | - Daniel L. Yule
- United States Geological Survey; Lake Superior Biological Station; 2800 Lakeshore Drive Ashland Wisconsin USA
| | - Trevor Middel
- Harkness Laboratory of Fisheries Research; Ontario Ministry of Natural Resources and Forestry; Trent University; 2140 East Bank Drive Peterborough Ontario Canada
| | - Paul Bentzen
- Department of Biology; Dalhousie University; 1355 Oxford St. Halifax Nova Scotia Canada
| | - Charles C. Krueger
- Center for Systems Integration and Sustainability; Michigan State University; 115 Manly Miles Building, 1405 South Harrison Road East Lansing Michigan USA
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52
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Fiera C, Habel JC, Kunz M, Ulrich W. Large-scale phylogenetic structure of European springtails (Collembola) depends on species range size and postglacial colonization history. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Cristina Fiera
- Institute of Biology; Romanian Academy; 296 Splaiul Independenţei PO Box 56-53 RO-060031 Bucharest Romania
| | - Jan Christian Habel
- Terrestrial Ecology Research Group; Department of Ecology and Ecosystem Management; Technische Universität München; D-85354 Freising-Weihenstephan Germany
| | - Mieczysław Kunz
- Department of Geomatics and Cartography; Nicolaus Copernicus University in Torun; Lwowska 1 PL-87-100 Toruń Poland
| | - Werner Ulrich
- Chair of Ecology and Biogeography; Nicolaus Copernicus University in Torun; Lwowska 1 PL-87-100 Toruń Poland
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53
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Baillie SM, Muir AM, Hansen MJ, Krueger CC, Bentzen P. Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush. BMC Evol Biol 2016; 16:219. [PMID: 27756206 PMCID: PMC5069848 DOI: 10.1186/s12862-016-0788-8] [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: 05/11/2016] [Accepted: 10/04/2016] [Indexed: 01/24/2023] Open
Abstract
Background Adaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycush that considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing. Results Four putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments. Conclusion We provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake in the world for a species that recently lost considerable genetic diversity and is now in recovery. Unknown is whether observed patterns are a result of an early stage of incipient speciation, gene flow-selection equilibrium, or reverse speciation causing formerly divergent ecotypes to collapse into a single gene pool. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0788-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shauna M Baillie
- Marine Gene Probe Lab, Department of Biology, Dalhousie University, 1355 Oxford Street, PO Box 15000, Halifax, NS, B3H 4R2, Canada.
| | - Andrew M Muir
- Great Lakes Fishery Commission, 2100 Commonwealth Boulevard, Ann Arbor, MI, 48105, USA
| | - Michael J Hansen
- U.S. Geological Survey, Great Lakes Science Center, Hammond Bay Biological Station, 11188 Ray Road, Millersburg, MI, 49759, USA
| | - Charles C Krueger
- Department of Fisheries and Wildlife, Center for Systems Integration and Sustainability, Michigan State University, East Lansing, MI, 48824-1222, USA
| | - Paul Bentzen
- Marine Gene Probe Lab, Department of Biology, Dalhousie University, 1355 Oxford Street, PO Box 15000, Halifax, NS, B3H 4R2, Canada
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54
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Chavarie L, Harford WJ, Howland KL, Fitzsimons J, Muir AM, Krueger CC, Tonn WM. Multiple generalist morphs of Lake Trout: Avoiding constraints on the evolution of intraspecific divergence? Ecol Evol 2016; 6:7727-7741. [PMID: 30128124 PMCID: PMC6093156 DOI: 10.1002/ece3.2506] [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: 04/26/2016] [Revised: 08/26/2016] [Accepted: 08/30/2016] [Indexed: 12/29/2022] Open
Abstract
A generalist strategy, as an adaptation to environmental heterogeneity, is common in Arctic freshwater systems, often accompanied, however, by intraspecific divergence that promotes specialization in niche use. To better understand how resources may be partitioned in a northern system that supports intraspecific diversity of Lake Trout, trophic niches were compared among four shallow‐water morphotypes in Great Bear Lake (N65° 56′ 39″, W120° 50′ 59″). Bayesian mixing model analyses of stable isotopes of carbon and nitrogen were conducted on adult Lake Trout. Major niche overlap in resource use among four Lake Trout morphotypes was found within littoral and pelagic zones, which raises the question of how such polymorphism can be sustained among opportunistic generalist morphotypes. Covariances of our morphological datasets were tested against δ13C and δ15N values. Patterns among morphotypes were mainly observed for δ15N. This link between ecological and morphological differentiation suggested that selection pressure(s) operate at the trophic level (δ15N), independent of habitat, rather than along the habitat‐foraging opportunity axis (δ13C). The spatial and temporal variability of resources in Arctic lakes, such as Great Bear Lake, may have favored the presence of multiple generalists showing different degrees of omnivory along a weak benthic–pelagic gradient. Morphs 1–3 had more generalist feeding habits using both benthic and pelagic habitats than Morph 4, which was a top‐predator specialist in the pelagic habitat. Evidence for frequent cannibalism in Great Bear Lake was found across all four morphotypes and may also contribute to polymorphism. We suggest that the multiple generalist morphs described here from Great Bear Lake are a unique expression of diversity due to the presumed constraints on the evolution of generalists and contrast with the development of multiple specialists, the standard response to intraspecific divergence.
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Affiliation(s)
- Louise Chavarie
- Center for Systems Integration and Sustainability Michigan State University East Lansing MI USA.,Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - William J Harford
- Cooperative Institute of Marine & Atmospheric Studies University of Miami Miami FL USA
| | - Kimberly L Howland
- Department of Biological Sciences University of Alberta Edmonton AB Canada.,Fisheries and Oceans Canada Winnipeg MB Canada
| | | | | | - Charles C Krueger
- Center for Systems Integration and Sustainability Michigan State University East Lansing MI USA
| | - William M Tonn
- Department of Biological Sciences University of Alberta Edmonton AB Canada
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55
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Bernatchez S, Laporte M, Perrier C, Sirois P, Bernatchez L. Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses. Mol Ecol 2016; 25:4773-92. [DOI: 10.1111/mec.13795] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 07/18/2016] [Accepted: 08/04/2016] [Indexed: 12/19/2022]
Affiliation(s)
- S. Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
| | - M. Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
| | - C. Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
- Centre d'Ecologie Fonctionnelle and Evolutive; CNRS; 34293 Montpellier 5 France
| | - P. Sirois
- Chaire de recherche sur les espèces aquatiques exploitées; Université du Québec à Chicoutimi; Chicoutimi Québec Canada G7H 2B1
| | - L. Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Québec Canada G1V 0A6
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56
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Fine-scale behavioural differences distinguish resource use by ecomorphs in a closed ecosystem. Sci Rep 2016; 6:24369. [PMID: 27098197 PMCID: PMC4838883 DOI: 10.1038/srep24369] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/16/2016] [Indexed: 11/19/2022] Open
Abstract
Temporal differences in habitat use and foraging specialisms between ecomorphs represent aspects of behavioural phenotype that are poorly understood with regard to the origin and maintenance of ecological diversity. We tested the role of behaviour in resource use divergence of two Arctic charr (Salvelinus alpinus) phenotypes, a slim, putatively pelagic-dwelling morph and a robust, putatively littoral-dwelling generalist morph, over an annual cycle, using biotelemetry and stable isotopes. Pelagic morph charr exhibited significantly greater δC13 depletion, concordant with increased zooplanktivory, than for the Littoral morph. Although three-dimensional space-use of the morphs strongly overlapped, on average, the Littoral morph used that habitat 19.3% more than the Pelagic morph. Pelagic morph fish were significantly more active, further from the lake bed and at greater depth than Littoral fish (annual means respectively, Pelagic, 0.069BLs−1, 8.21 m and 14.11 m; Littoral, 0.047BLs−1, 5.87 m and 10.47 m). Patterns of habitat use differed between ecomorphs at key times, such as during autumn and at ice break, likely related to spawning and resumption of intensive foraging respectively. Extensive space-use overlap, but fine-scale differences in habitat use between charr ecomorphs, suggests the importance of competition for generating and maintaining polymorphism, and its potential for promoting reproductive isolation and evolution in sympatry.
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57
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Adams CE, Bean CW, Dodd JA, Down A, Etheridge EC, Gowans ARD, Hooker O, Knudsen R, Lyle AA, Winfield IJ, Præbel K. Inter and intra-population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus, a rare freshwater fish in Scotland. JOURNAL OF FISH BIOLOGY 2016; 88:580-594. [PMID: 26748995 DOI: 10.1111/jfb.12855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
This study revealed between-lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (FST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common-garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (FST = 0·001-0·024) and evidence of private alleles related to the basin structure of the lake. Within-lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.
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Affiliation(s)
- C E Adams
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - C W Bean
- Scottish Natural Heritage, Caspian House, Clydebank Business Park, Clydebank, Glasgow G81 2NR, U.K
| | - J A Dodd
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - A Down
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - E C Etheridge
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - A R D Gowans
- Environment Agency, Ghyll Mount, Gillan Way, Penrith 40 Business Park, Penrith, Cumbria CA11 9BP, U.K
| | - O Hooker
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - R Knudsen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - A A Lyle
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - I J Winfield
- Lake Ecosystems Group, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, U.K
| | - K Præbel
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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58
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Otolith variation in Pacific herring (Clupea pallasii) reflects mitogenomic variation rather than the subspecies classification. Polar Biol 2016. [DOI: 10.1007/s00300-015-1882-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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59
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Rougemont Q, Gaigher A, Lasne E, Côte J, Coke M, Besnard AL, Launey S, Evanno G. Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys. J Evol Biol 2015; 28:2248-63. [PMID: 26348652 DOI: 10.1111/jeb.12750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 01/10/2023]
Abstract
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here, we used a combination of mating trials, experimental crosses and population genetic analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (Lampetra planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size-assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically based divergent selection may explain these variable levels of divergence among sympatric population pairs, but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress towards speciation.
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Affiliation(s)
- Q Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - A Gaigher
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France.,Laboratory for Conservation Biology, Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - E Lasne
- Muséum National d'Histoire Naturelle, CRESCO, Dinard, France.,UMR CARRTEL, INRA, Thonon-les-Bains, France
| | - J Côte
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - M Coke
- Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique, INRA, Rennes, France
| | - A-L Besnard
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - S Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - G Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
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60
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Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol Ecol 2015; 24:3421-40. [PMID: 25997156 PMCID: PMC4973668 DOI: 10.1111/mec.13247] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022]
Abstract
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.
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Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, Bern, 3005, Switzerland
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Timothee Cezard
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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61
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Nested Levels of Adaptive Divergence: The Genetic Basis of Craniofacial Divergence and Ecological Sexual Dimorphism. G3-GENES GENOMES GENETICS 2015; 5:1613-24. [PMID: 26038365 PMCID: PMC4528318 DOI: 10.1534/g3.115.018226] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exemplary systems for adaptive divergence are often characterized by their large degrees of phenotypic variation. This variation represents the outcome of generations of diversifying selection. However, adaptive radiations can also contain a hierarchy of differentiation nested within them where species display only subtle phenotypic differences that still have substantial effects on ecology, function, and ultimately fitness. Sexual dimorphisms are also common in species displaying adaptive divergence and can be the result of differential selection between sexes that produce ecological differences between sexes. Understanding the genetic basis of subtle variation (between certain species or sexes) is therefore important for understanding the process of adaptive divergence. Using cichlids from the dramatic adaptive radiation of Lake Malawi, we focus on understanding the genetic basis of two aspects of relatively subtle phenotypic variation. This included a morphometric comparison of the patterns of craniofacial divergence between two ecologically similar species in relation to the larger adaptive radiation of Malawi, and male-female morphological divergence between their F2 hybrids. We then genetically map craniofacial traits within the context of sex and locate several regions of the genome that contribute to variation in craniofacial shape that is relevant to sexual dimorphism within species and subtle divergence between closely related species, and possibly to craniofacial divergence in the Malawi radiation as a whole. To enhance our search for candidate genes we take advantage of population genomic data and a genetic map that is anchored to the cichlid genome to determine which genes within our QTL regions are associated with SNPs that are alternatively fixed between species. This study provides a holistic understanding of the genetic underpinnings of adaptive divergence in craniofacial shape.
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62
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Ozerov MY, Himberg M, Aykanat T, Sendek DS, Hägerstrand H, Verliin A, Krause T, Olsson J, Primmer CR, Vasemägi A. Generation of a neutral F
ST
baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin. J Evol Biol 2015; 28:1170-83. [DOI: 10.1111/jeb.12645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/17/2023]
Affiliation(s)
- M. Y. Ozerov
- Department of Biology; University of Turku; Turku Finland
| | - M. Himberg
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - T. Aykanat
- Department of Biology; University of Turku; Turku Finland
| | - D. S. Sendek
- State Research Institute on Lake and River Fisheries (GosNIORKh); St. Petersburg Russia
| | - H. Hägerstrand
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - A. Verliin
- Estonian Marine Institute; University of Tartu; Tartu Estonia
| | - T. Krause
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
| | - J. Olsson
- Department of Aquatic Resources; Institute for Coastal Research; Swedish University of Agricultural Sciences; Öregrund Sweden
| | - C. R. Primmer
- Department of Biology; University of Turku; Turku Finland
| | - A. Vasemägi
- Department of Biology; University of Turku; Turku Finland
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
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63
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Kolář F, Píšová S, Záveská E, Fér T, Weiser M, Ehrendorfer F, Suda J. The origin of unique diversity in deglaciated areas: traces of Pleistocene processes in north-European endemics from theGalium pusillumpolyploid complex (Rubiaceae). Mol Ecol 2015; 24:1311-34. [DOI: 10.1111/mec.13110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Filip Kolář
- National Centre for Biosystematics, Natural History Museum; University of Oslo; Oslo NO-0318 Norway
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
| | - Soňa Píšová
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
| | - Eliška Záveská
- Institute of Botany; University of Innsbruck; Sternwartestraße 15 Innsbruck A-6020 Austria
| | - Tomáš Fér
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
| | - Martin Weiser
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
| | - Friedrich Ehrendorfer
- Department of Systematic and Evolutionary Botany; Faculty Centre for Biodiversity; University of Vienna; Rennweg 14 Vienna A-1030 Austria
| | - Jan Suda
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
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64
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McKinney GJ, Varian A, Scardina J, Nichols KM. Genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis commonly stocked in Lake Superior. PLoS One 2014; 9:e113809. [PMID: 25479612 PMCID: PMC4257586 DOI: 10.1371/journal.pone.0113809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/30/2014] [Indexed: 11/19/2022] Open
Abstract
Fitness related traits often show spatial variation across populations of widely distributed species. Comparisons of genetic variation among populations in putatively neutral DNA markers and in phenotypic traits susceptible to selection (QST FST analysis) can be used to determine to what degree differentiation among populations can be attributed to selection or genetic drift. Traditionally, QST FST analyses require a large number of populations to achieve sufficient statistical power; however, new methods have been developed that allow QST FST comparisons to be conducted on as few as two populations if their pedigrees are informative. This study compared genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis that were historically or currently used for stocking in the Lake Superior Basin. Herein we examined if morphological divergence among populations showed temporal variation, and if divergence could be attributed to selection or was indistinguishable from genetic drift. Multivariate QST FST analysis showed evidence for divergent selection between populations. Univariate analyses suggests that the pattern observed in the multivariate analyses was largely driven by divergent selection for length and weight, and moreover by divergence between the Assinica strain and each of the Iron River and Siskiwit strains rather than divergent selection between each population pair. While it could not be determined if divergence was due to natural selection or inadvertent artificial selection in hatcheries, selected differences were consistent with patterns of domestication commonly found in salmonids.
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Affiliation(s)
- Garrett J. McKinney
- Purdue University, Department of Biological Sciences, West Lafayette, Indiana, United States of America
| | - Anna Varian
- Purdue University, Department of Forestry and Natural Resources, West Lafayette, Indiana, United States of America
| | - Julie Scardina
- Purdue University, Department of Biological Sciences, West Lafayette, Indiana, United States of America
| | - Krista M. Nichols
- Purdue University, Department of Biological Sciences, West Lafayette, Indiana, United States of America
- * E-mail:
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Kahilainen KK, Patterson WP, Sonninen E, Harrod C, Kiljunen M. Adaptive radiation along a thermal gradient: preliminary results of habitat use and respiration rate divergence among whitefish morphs. PLoS One 2014; 9:e112085. [PMID: 25405979 PMCID: PMC4236043 DOI: 10.1371/journal.pone.0112085] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/13/2014] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiation is considered an important mechanism for the development of new species, but very little is known about the role of thermal adaptation during this process. Such adaptation should be especially important in poikilothermic animals that are often subjected to pronounced seasonal temperature variation that directly affects metabolic function. We conducted a preliminary study of individual lifetime thermal habitat use and respiration rates of four whitefish (Coregonus lavaretus (L.)) morphs (two pelagic, one littoral and one profundal) using stable carbon and oxygen isotope values of otolith carbonate. These morphs, two of which utilized pelagic habitats, one littoral and one profundal recently diverged via adaptive radiation to exploit different major niches in a deep and thermally stratified subarctic lake. We found evidence that the morphs used different thermal niches. The profundal morph had the most distinct thermal niche and consistently occupied the coldest thermal habitat of the lake, whereas differences were less pronounced among the shallow water pelagic and littoral morphs. Our results indicated ontogenetic shifts in thermal niches: juveniles of all whitefish morphs inhabited warmer ambient temperatures than adults. According to sampling of the otolith nucleus, hatching temperatures were higher for benthic compared to pelagic morphs. Estimated respiration rate was the lowest for benthivorous profundal morph, contrasting with the higher values estimated for the other morphs that inhabited shallower and warmer water. These preliminary results suggest that physiological adaptation to different thermal habitats shown by the sympatric morphs may play a significant role in maintaining or strengthening niche segregation and divergence in life-history traits, potentially contributing to reproductive isolation and incipient speciation.
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Affiliation(s)
- Kimmo Kalevi Kahilainen
- Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, Finland
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - William Paul Patterson
- Department of Geological Sciences, Saskatchewan, Isotope Laboratory, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Eloni Sonninen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Chris Harrod
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Mikko Kiljunen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada's Great Bear Lake. Heredity (Edinb) 2014; 114:94-106. [PMID: 25204304 DOI: 10.1038/hdy.2014.74] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/24/2014] [Accepted: 07/14/2014] [Indexed: 11/09/2022] Open
Abstract
Range expansion in north-temperate fishes subsequent to the retreat of the Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited, heterogeneous habitats and, in many situations, secondary contact among conspecific lineages that were once previously isolated. Such ecological opportunity coupled with reduced competition likely promoted morphological and genetic differentiation within and among post-glacial fish populations. Discrete morphological forms existing in sympatry, for example, have now been described in many species, yet few studies have directly assessed the association between morphological and genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are found in several large-lake systems including Great Bear Lake (GBL), Northwest Territories, Canada, where several shallow-water forms are known. Here, we assess microsatellite and mitochondrial DNA variation among four morphotypes of Lake Trout from the five distinct arms of GBL, and also from locations outside of this system to evaluate several hypotheses concerning the evolution of morphological variation in this species. Our data indicate that morphotypes of Lake Trout from GBL are genetically differentiated from one another, yet the morphotypes are still genetically more similar to one another compared with populations from outside of this system. Furthermore, our data suggest that Lake Trout colonized GBL following dispersal from a single glacial refugium (the Mississippian) and support an intra-lake model of divergence. Overall, our study provides insights into the origins of morphological and genetic variation in post-glacial populations of fishes and provides benchmarks important for monitoring Lake Trout biodiversity in a region thought to be disproportionately susceptible to impacts from climate change.
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Dierking J, Phelps L, Præbel K, Ramm G, Prigge E, Borcherding J, Brunke M, Eizaguirre C. Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.). Evol Appl 2014; 7:1068-83. [PMID: 25553068 PMCID: PMC4231596 DOI: 10.1111/eva.12166] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/30/2014] [Indexed: 11/27/2022] Open
Abstract
Natural hybridization plays a key role in the process of speciation. However, anthropogenic (human induced) hybridization of historically isolated taxa raises conservation issues. Due to weak barriers to gene flow and the presence of endangered taxa, the whitefish species complex is an excellent study system to investigate the consequences of hybridization in conservation. We focused on three naturally reproductively isolated whitefish taxa in Germany: the endangered, anadromous North Sea houting (NSH) and Baltic houting (BH), which were reintroduced after local extinction, and the commercially stocked European whitefish (EW). To evaluate the genetic integrity of each taxon, source and reintroduced populations of NSH and BH, and EW populations were characterized based on two mitochondrial and 17 microsatellite loci. Additionally, we investigated gill raker counts as an adaptive phenotypic trait. Even though clear genetic and phenotypic differentiation confirmed the houtings as separate evolutionarily significant units, admixture analyses revealed an extensive hybrid zone. Hybridizations were introgressive, positively correlated with genetic diversity, and were reflected in the gill raker counts. The BH distribution range showed higher heterogeneity and stronger admixture than the NSH range. Erroneous stocking with non-native genotypes best explained these patterns, which pose challenges for the conservation of the endangered NSH and BH.
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Affiliation(s)
- Jan Dierking
- Research Division Marine Ecology, Research Unit Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Luke Phelps
- Research Division Marine Ecology, Research Unit Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany ; Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Kim Præbel
- Department of Arctic and Marine Biology, Faculty of Biosciences Fisheries and Economics, University of Tromsø Tromsø, Norway
| | - Gesine Ramm
- Research Division Marine Ecology, Research Unit Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany ; Faculty of Science, University of Copenhagen Frederiksberg, Denmark
| | - Enno Prigge
- Research Division Marine Ecology, Research Unit Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Jost Borcherding
- General Ecology & Limnology, Ecological Research Station Grietherbusch, Zoological Institute of the University of Cologne Cologne, Germany
| | - Matthias Brunke
- Landesamt für Landwirtschaft, Umwelt und ländliche Räume (LLUR) Flintbek, Germany
| | - Christophe Eizaguirre
- Research Division Marine Ecology, Research Unit Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
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68
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Evans ML, Praebel K, Peruzzi S, Amundsen PA, Bernatchez L. Phenotype-environment association of the oxygen transport system in trimorphic European whitefish (Coregonus lavaretus) populations. Evolution 2014; 68:2197-210. [PMID: 24766154 DOI: 10.1111/evo.12442] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/17/2014] [Indexed: 01/20/2023]
Abstract
Replicated adaptive radiation events, typified by phenotypic divergence across resource axes, provide important insight into the eco-evolutionary dynamics that lead to the formation of new species. Here, we show that in trimorphic adaptive radiations of European whitefish (Coregonus lavaretus), divergence of the oxygen transport system has occurred across the pelagic/littoral (shallow)-profundal (deep) resource axis, and at multiple biological scales. Profundal whitefish exhibited significantly larger red blood cells (RBCs), a greater proportion of cathodic hemoglobin protein components, and higher hemoglobin transcript abundance in kidney compared to littoral and pelagic morphs. Hemoglobin transcript abundance in brain and gill, but not kidney, and anodic hemoglobin protein component diversity in blood were also linked to variation at an intronic single nucleotide polymorphism (SNP). As the whitefish morphs differ in population genetic structure at this SNP, hemoglobin transcript and protein divergence between profundal and pelagic/littoral morphs is likely being driven by genetic divergence. Our findings, along with our previous work on lake whitefish, highlight the importance of the oxygen transport system to the postglacial colonization of novel lacustrine environments by whitefish throughout the northern hemisphere.
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Affiliation(s)
- Melissa L Evans
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Université Laval, Québec, Québec, G1V 0A6 Canada; Present Address: Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, 2030 SE Marine Science Dr, Newport, Oregon 97365.
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69
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Bhat S, Amundsen PA, Knudsen R, Gjelland KØ, Fevolden SE, Bernatchez L, Præbel K. Speciation reversal in European whitefish (Coregonus lavaretus (L.)) caused by competitor invasion. PLoS One 2014; 9:e91208. [PMID: 24626131 PMCID: PMC3953381 DOI: 10.1371/journal.pone.0091208] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 02/10/2014] [Indexed: 11/19/2022] Open
Abstract
Invasion of exotic species has caused the loss of biodiversity and imparts evolutionary and ecological changes in the introduced systems. In northern Fennoscandia, European whitefish (Coregonus lavaretus (L.)) is a highly polymorphic species displaying adaptive radiations into partially reproductively isolated and thus genetically differentiated sympatric morphs utilizing the planktivorous and benthivorous food niche in many lakes. In 1993, Lake Skrukkebukta was invaded by vendace (Coregonus albula (L.)) which is a zooplanktivorous specialist. The vendace displaced the densely rakered whitefish from its preferred pelagic niche to the benthic habitat harbouring the large sparsely rakered whitefish. In this study, we investigate the potential influence of the vendace invasion on the breakdown of reproductive isolation between the two whitefish morphs. We inferred the genotypic and phenotypic differentiation between the two morphs collected at the arrival (1993) and 15 years after (2008) the vendace invasion using 16 microsatellite loci and gill raker numbers, the most distinctive adaptive phenotypic trait between them. The comparison of gill raker number distributions revealed two modes growing closer over 15 years following the invasion. Bayesian analyses of genotypes revealed that the two genetically distinct whitefish morphs that existed in 1993 had collapsed into a single population in 2008. The decline in association between the gill raker numbers and admixture values over 15 years corroborates the findings from the Bayesian analysis. Our study thus suggests an apparent decrease of reproductive isolation in a morph-pair of European whitefish within 15 years (≃ 3 generations) following the invasion of a superior trophic competitor (vendace) in a subarctic lake, reflecting a situation of "speciation in reverse".
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Affiliation(s)
- Shripathi Bhat
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Per-Arne Amundsen
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Rune Knudsen
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | | | - Svein-Erik Fevolden
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Kim Præbel
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
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70
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Siwertsson A, Knudsen R, Adams CE, Præbel K, Amundsen PA. Parallel and non-parallel morphological divergence among foraging specialists in European whitefish (Coregonus lavaretus). Ecol Evol 2013; 3:1590-602. [PMID: 23789070 PMCID: PMC3686194 DOI: 10.1002/ece3.562] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 11/19/2022] Open
Abstract
Parallel phenotypic evolution occurs when independent populations evolve similar traits in response to similar selective regimes. However, populations inhabiting similar environments also frequently show some phenotypic differences that result from non-parallel evolution. In this study, we quantified the relative importance of parallel evolution to similar foraging regimes and non-parallel lake-specific effects on morphological variation in European whitefish (Coregonus lavaretus). We found evidence for both lake-specific morphological characteristics and parallel morphological divergence between whitefish specializing in feeding on profundal and littoral resources in three separate lakes. Foraging specialists expressed similar phenotypes in different lakes in both overall body shape and selected measured morphological traits. The morphology of the two whitefish specialists resembled that predicted from other fish species, supporting the conclusion of an adaptive significance of the observed morphological characteristics. Our results indicate that divergent natural selection resulting from foraging specialization is driving and/or maintaining the observed parallel morphological divergence. Whitefish in this study may represent an early stage of divergence towards the evolution of specialized morphs.
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Affiliation(s)
- Anna Siwertsson
- Department of Arctic and Marine Biology, University of Tromsø N-9037 Tromsø, Norway
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