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Kroes R, Winkel Y, Breeuwer JAJ, van Loon EE, Loader SP, Maclaine JS, Verdonschot PFM, van der Geest HG. Phylogenetic analysis of museum specimens of houting Coregonus oxyrinchus shows the need for a revision of its extinct status. BMC Ecol Evol 2023; 23:57. [PMID: 37752477 PMCID: PMC10523663 DOI: 10.1186/s12862-023-02161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
According to the IUCN Red List the anadromous houting Coregonus oxyrinchus is categorized as 'extinct'. However, this extinct status might be incorrect because taxonomic difference between C. oxyrinchus and the closely related C. lavaretus is based on a disputable morphological comparison. Also, phylogenetic studies on mtDNA only focused on recent obtained coregonids. We are the first to perform a mtDNA analysis on both historic and recent specimens, including the syntype specimen which was used for species description by Linnaeus originally. Two primer pairs for mitochondrial CytB and ND3 were used to extract sequences for phylogenetic analysis. Sequences from 14 out of 21 C. oxyrinchus museum specimens were successfully obtained and compared with sequences from recent obtained C. lavaretus. The sequences were combined with GenBank data from a previous phylogenetic study on houting to create a phylogenetic tree and two minimum spanning haplotype networks. Results show that C. oxyrinchus and C. lavaretus form a clade with limited genetic variation. Low bootstrap values also show weak support for geographical patterns in distribution of mitochondrial haplotypes. Statistical analysis of the haplotype networks also shows that historic and recent specimens are similar species. Our results suggest that C. oxyrinchus is a junior synonym of C. lavaretus. A definitive taxonomic revision could not be made because only CytB sequencing was successful for the syntype specimen. We discuss taxonomic consequences and the species-specific focus in nature conservation. We propose a shift in nature conservation to a more functional approach based on traits rather than species.
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Affiliation(s)
- R Kroes
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.
| | - Y Winkel
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - J A J Breeuwer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - E E van Loon
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - S P Loader
- Natural History Museum, Cromwell Rd, South Kensington, London, SW7 5BD, UK
| | - J S Maclaine
- Natural History Museum, Cromwell Rd, South Kensington, London, SW7 5BD, UK
| | - P F M Verdonschot
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3-3 A, Wageningen, 6708 PB, The Netherlands
| | - H G van der Geest
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
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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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Häkli K, Østbye K, Kahilainen KK, Amundsen P, Præbel K. Diversifying selection drives parallel evolution of gill raker number and body size along the speciation continuum of European whitefish. Ecol Evol 2018; 8:2617-2631. [PMID: 29531681 PMCID: PMC5838045 DOI: 10.1002/ece3.3876] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 12/11/2022] Open
Abstract
Adaptive radiation is the evolution of ecological and phenotypical diversity. It arises via ecological opportunity that promotes the exploration of underutilized or novel niches mediating specialization and reproductive isolation. The assumed precondition for rapid local adaptation is diversifying natural selection, but random genetic drift could also be a major driver of this process. We used 27 populations of European whitefish (Coregonus lavaretus) from nine lakes distributed in three neighboring subarctic watercourses in northern Fennoscandia as a model to test the importance of random drift versus diversifying natural selection for parallel evolution of adaptive phenotypic traits. We contrasted variation for two key adaptive phenotypic traits correlated with resource utilization of polymorphic fish; the number of gill rakers and the total length of fish, with the posterior distribution of neutral genetic differentiation from 13 microsatellite loci, to test whether the observed phenotypic divergence could be achieved by random genetic drift alone. Our results show that both traits have been under diversifying selection and that the evolution of these morphs has been driven by isolation through habitat adaptations. We conclude that diversifying selection acting on gill raker number and body size has played a significant role in the ongoing adaptive radiation of European whitefish morphs in this region.
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Affiliation(s)
- Katja Häkli
- Faculty of Biosciences, Fisheries and EconomicsNorwegian College of Fishery ScienceUiT The Arctic University of NorwayTromsøNorway
| | - Kjartan Østbye
- Faculty of Applied Ecology and Agricultural SciencesHedmark University of Applied ScienceElverumNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloOsloNorway
| | - Kimmo K. Kahilainen
- Faculty of Biosciences, Fisheries and EconomicsNorwegian College of Fishery ScienceUiT The Arctic University of NorwayTromsøNorway
| | - Per‐Arne Amundsen
- Department of Arctic and Marine BiologyFaculty of Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
| | - Kim Præbel
- Faculty of Biosciences, Fisheries and EconomicsNorwegian College of Fishery ScienceUiT The Arctic University of NorwayTromsøNorway
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4
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Crisci C, Ledoux JB, Mokhtar-Jamaï K, Bally M, Bensoussan N, Aurelle D, Cebrian E, Coma R, Féral JP, La Rivière M, Linares C, López-Sendino P, Marschal C, Ribes M, Teixidó N, Zuberer F, Garrabou J. Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species. Sci Rep 2017; 7:5069. [PMID: 28698582 PMCID: PMC5505982 DOI: 10.1038/s41598-017-05220-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/25/2017] [Indexed: 11/20/2022] Open
Abstract
The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitat-forming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 °C as a critical thermal threshold. After one week of exposure at this temperature, seven of the eight populations were affected by tissue necrosis and after 30 days of exposure at this temperature, the mean % of affected colonies increased gradually from 3 to 97%. We then demonstrate the weak relation between the observed differential phenotypic responses and the local temperature regimes experienced by each population. A significant correlation was observed between these responses and the extent of genetic drift impacting each population. Local adaptation may thus be hindered by genetic drift, which seems to be the main driver of the differential response. Accordingly, conservation measures should promote connectivity and control density erosion in order to limit the impact of genetic drift on marine populations facing climate change.
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Affiliation(s)
- C Crisci
- Polo de Desarrollo Universitario Modelización y Análisis de Recursos Naturales, Centro Universitario Regional del Este, Universidad de la República, Rocha, 27000, Uruguay.
| | - J-B Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, 4050-123, Portugal
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - K Mokhtar-Jamaï
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M Bally
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
| | - N Bensoussan
- IPSO FACTO, SCOPArl, Pole Océanologie, Marseille, 13001, France
| | - D Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - E Cebrian
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, 17300, Spain
- Departament de Ciències Ambientals, Facultat de Ciències, Universitat de Girona, Girona, 17071, Spain
| | - R Coma
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, 17300, Spain
| | - J-P Féral
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M La Rivière
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
| | - C Linares
- Departament d'Ecologia, Universitat de Barcelona, Barcelona, 08028, Spain
| | - P López-Sendino
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - C Marschal
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M Ribes
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - N Teixidó
- Stazione Zoologica Anton Dohrn, Villa Dohrn-Benthic Ecology Center, Punta San Pietro, Ischia, Naples, 80077, Italy
| | - F Zuberer
- Institut Pytheas, UMS 3470, CNRS, Marseille, 13013, France
| | - J Garrabou
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
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Bankers L, Fields P, McElroy KE, Boore JL, Logsdon JM, Neiman M. Genomic evidence for population-specific responses to co-evolving parasites in a New Zealand freshwater snail. Mol Ecol 2017; 26:3663-3675. [PMID: 28429458 DOI: 10.1111/mec.14146] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/13/2023]
Abstract
Reciprocal co-evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co-evolving host-parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its co-evolving sterilizing trematode parasite, Microphallus sp., a textbook example of natural coevolution. We found that Microphallus-infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population-level co-evolution is leading to population-specific host-parasite interactions and evolutionary trajectories. We also used an FST -based approach to identify a set of loci that represent promising candidates for targets of parasite-mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population-specific responses to co-evolving infection in the P. antipodarum-Microphallus interaction and provide new insights into the genomic basis of co-evolutionary interactions in nature.
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Affiliation(s)
- Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Peter Fields
- Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - Kyle E McElroy
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jeffrey L Boore
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
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Aykanat T, Lindqvist M, Pritchard VL, Primmer CR. From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2016; 89:2658-2679. [PMID: 27709620 DOI: 10.1111/jfb.13149] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species.
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Affiliation(s)
- T Aykanat
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - M Lindqvist
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - V L Pritchard
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - C R Primmer
- Department of Biology, University of Turku, Turku, 20014, Finland
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Flanagan SP, Rose E, Jones AG. Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish. Mol Ecol 2016; 25:5043-5072. [DOI: 10.1111/mec.13794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Sarah P. Flanagan
- Biology Department Texas A&M University College Station TX 77843 USA
| | - Emily Rose
- Biology Department Texas A&M University College Station TX 77843 USA
| | - Adam G. Jones
- Biology Department Texas A&M University College Station TX 77843 USA
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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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Li SL, Vasemägi A, Ramula S. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader. ANNALS OF BOTANY 2016; 117:187-194. [PMID: 26420202 PMCID: PMC4701146 DOI: 10.1093/aob/mcv145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND AIMS Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. METHODS Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. KEY RESULTS It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. CONCLUSIONS The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity.
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Affiliation(s)
- Shou-Li Li
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA,
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia and
| | - Satu Ramula
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Aronia Coastal Zone Research Team, Åbo Akademi University and Novia University of Applied Sciences, Raseborgsvägen 9, 10600 Ekenäs, Finland
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RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs. G3-GENES GENOMES GENETICS 2015; 5:1481-91. [PMID: 26002924 PMCID: PMC4502382 DOI: 10.1534/g3.115.019067] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site−associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.
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