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Coll-Costa C, Dahms C, Kemppainen P, Alexandre CM, Ribeiro F, Zanella D, Zanella L, Merilä J, Momigliano P. Parallel evolution despite low genetic diversity in three-spined sticklebacks. Proc Biol Sci 2024; 291:20232617. [PMID: 38593844 PMCID: PMC11003780 DOI: 10.1098/rspb.2023.2617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback (Gasterosteus aculeatus) repeatedly colonized and adapted to brackish and freshwater. Most parallel evolution studies in G. aculeatus were conducted at high latitudes, where freshwater populations maintain connectivity to the source marine populations. Here, we analysed southern and northern European marine and freshwater populations to test two hypotheses. First, that southern European freshwater populations (which currently lack connection to marine populations) lost genetic diversity due to bottlenecks and inbreeding compared to their northern counterparts. Second, that the degree of genetic parallelism is higher among northern than southern European freshwater populations, as the latter have been subjected to strong drift due to isolation. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss probably happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.
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Affiliation(s)
- Carla Coll-Costa
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Carolin Dahms
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Petri Kemppainen
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Carlos M. Alexandre
- MARE—Marine and Environmental Sciences Centre, Universidade de Évora, Évora, 7004-516, Portugal
| | - Filipe Ribeiro
- MARE—Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Davor Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Linda Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Paolo Momigliano
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
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2
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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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3
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Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: the genomic basis of environmental adaptation in house mice ( Mus musculus domesticus) from the Americas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564674. [PMID: 37961195 PMCID: PMC10634997 DOI: 10.1101/2023.10.30.564674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Parallel clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in regulatory regions. Genes containing the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, and development or function of the eye as well as traits associated with the cardiovascular and renal systems. We then combined these results with published results from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects, providing strong evidence of parallel adaptation and identifying genes that likely underlie recent environmental adaptation in house mice across North and South America.
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Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, United States of America
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4
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Lajmi A, Glinka F, Privman E. Optimizing ddRAD sequencing for population genomic studies with ddgRADer. Mol Ecol Resour 2023. [PMID: 37732396 DOI: 10.1111/1755-0998.13870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.
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Affiliation(s)
- Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Felix Glinka
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
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5
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Dean LL, Magalhaes IS, D’Agostino D, Hohenlohe P, MacColl ADC. On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback. Mol Biol Evol 2023; 40:msad191. [PMID: 37652053 PMCID: PMC10490448 DOI: 10.1093/molbev/msad191] [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: 03/02/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel Santos Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Department of Life Sciences, School of Health and Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Daniele D’Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Water Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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6
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Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F, Rogan E, Rosel PE, Sinding MHS, van der Es H, Wales N, Fontaine MC, Gaggiotti OE, Foote AD. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nat Commun 2023; 14:4020. [PMID: 37463880 DOI: 10.1038/s41467-023-39532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
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Affiliation(s)
- Marie Louis
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Greenland Institute of Natural Resources, Kivioq 2, Nuuk, 3900, Greenland.
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Milaja Nykänen
- Department of Environmental and Biological Sciences, PO Box 111, FI-80101, Joensuu, Finland
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Frederick Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Klaas Post
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA, 70506, USA
| | - Mikkel-Holger S Sinding
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Henry van der Es
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Nathan Wales
- University of York, BioArCh, Environment Building, Wentworth Way, Heslington, York, YO10 5DD, UK
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) Institut de Recherche pour le Développement (IRD), F-34394, Montpellier, France
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
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7
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Moreira LR, Smith BT. Convergent genomic signatures of local adaptation across a continental-scale environmental gradient. SCIENCE ADVANCES 2023; 9:eadd0560. [PMID: 37205757 PMCID: PMC10198635 DOI: 10.1126/sciadv.add0560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 04/17/2023] [Indexed: 05/21/2023]
Abstract
Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.
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Affiliation(s)
- Lucas R. Moreira
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
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8
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Moran RL, Richards EJ, Ornelas-García CP, Gross JB, Donny A, Wiese J, Keene AC, Kowalko JE, Rohner N, McGaugh SE. Selection-driven trait loss in independently evolved cavefish populations. Nat Commun 2023; 14:2557. [PMID: 37137902 PMCID: PMC10156726 DOI: 10.1038/s41467-023-37909-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.
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Affiliation(s)
- Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA.
- Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Emilie J Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Claudia Patricia Ornelas-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior S/N. CP 04510, D. F. México, México City, México
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Alexandra Donny
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular & Integrative Physiology, KU Medical Center, Kansas City, KS, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
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9
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Osborne OG, Dobreva MP, Papadopulos AST, de Moura MSB, Brunello AT, de Queiroz LP, Pennington RT, Lloyd J, Savolainen V. Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing. THE NEW PHYTOLOGIST 2023; 238:1305-1317. [PMID: 36444527 DOI: 10.1111/nph.18645] [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: 08/09/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.
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Affiliation(s)
- Owen G Osborne
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Mariya P Dobreva
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
| | - Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Magna S B de Moura
- Empresa Brasileira de Pesquisa Agropecuária, 56302-970, Petrolina, PE, Brazil
| | - Alexandre T Brunello
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, 14040-901, Ribeirão Preto, SP, Brazil
| | - Luciano P de Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, 44036-900, Feira de Santana, BA, Brazil
| | - R Toby Pennington
- Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Jon Lloyd
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Vincent Savolainen
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
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10
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Poore HA, Stuart YE, Rennison DJ, Roesti M, Hendry AP, Bolnick DI, Peichel CL. Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution 2023; 77:110-122. [PMID: 36622692 DOI: 10.1093/evolut/qpac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 01/10/2023]
Abstract
Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.
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Affiliation(s)
- Hilary A Poore
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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11
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Begum M, Nolan V, MacColl ADC. Ecological constraint, rather than opportunity, promotes adaptive radiation in three-spined stickleback ( Gasterosteus aculeatus) on North Uist. Ecol Evol 2023; 13:e9716. [PMID: 36644706 PMCID: PMC9831901 DOI: 10.1002/ece3.9716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
The context and cause of adaptive radiations have been widely described and explored but why rapid evolutionary diversification does not occur in related evolutionary lineages has yet to be understood. The standard answer is that evolutionary diversification is provoked by ecological opportunity and that some lineages do not encounter the opportunity. Three-spined sticklebacks on the Scottish island of North Uist show enormous diversification, which seems to be associated with the diversity of aquatic habitats. Sticklebacks on the neighboring island of South Uist have not been reported to show the same level of evolutionary diversity, despite levels of environmental variation that we might expect to be similar to North Uist. In this study, we compared patterns of morphological and environmental diversity on North and South Uist. Ancestral anadromous sticklebacks from both islands exhibited similar morphology including size and bony "armor." Resident sticklebacks showed significant variation in armor traits in relation to pH of water. However, North Uist sticklebacks exhibited greater diversity of morphological traits than South Uist and this was associated with greater diversity in pH of the waters of lochs on North Uist. Highly acidic and highly alkaline freshwater habitats are missing, or uncommon, on South Uist. Thus, pH appears to act as a causal factor driving the evolutionary diversification of stickleback in local adaptation in North and South Uist. This is consistent with diversification being more associated with ecological constraint than ecological opportunity.
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Affiliation(s)
- Mahmuda Begum
- School of Life SciencesUniversity of NottinghamNottinghamUK,Zoology Section, Biological Research DivisionBangladesh Council of Scientific & Industrial Research (BCSIR)DhakaBangladesh
| | - Victoria Nolan
- School of Life SciencesUniversity of NottinghamNottinghamUK
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12
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Strickland K, Räsänen K, Kristjánsson BK, Phillips JS, Einarsson A, Snorradóttir RG, Bartrons M, Jónsson ZO. Genome-phenotype-environment associations identify signatures of selection in a panmictic population of threespine stickleback. Mol Ecol 2023; 32:1708-1725. [PMID: 36627230 DOI: 10.1111/mec.16845] [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: 07/14/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023]
Abstract
Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here, we integrate whole-genome sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome wide divergence, yet multiple traits (body size, gill raker structure and defence traits) were divergent along known ecological gradients (temperature, predatory bird densities and water depth). SNP based heritability of all measured traits was high (h2 = 0.42-0.65), indicating adaptive potential for all traits. Environment-association analyses further identified thousands of loci putatively involved in selection, related to genes linked to, for instance, neuron development and protein phosphorylation. Finally, we found that loci linked to water depth were concurrently associated with pelvic spine length variation - supporting the conclusion that divergence in pelvic spine length occurred in the face of gene flow. Our results suggest that whilst there is substantial genetic variation in the traits measured, phenotypic divergence of Mývatn stickleback is mostly weakly associated with environmental gradients, potentially as a result of substantial gene flow. Our study illustrates the value of integrative studies that combine genomic assays of multivariate trait variation with landscape genomics.
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Affiliation(s)
- Kasha Strickland
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | - Katja Räsänen
- Department of Aquatic Ecology, EAWAG and Institute of Integrative Biology, ETH, Zurich, Switzerland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | - Joseph S Phillips
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland.,Department of Biology, Creighton University, Omaha, Nebraska, USA
| | | | - Ragna G Snorradóttir
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | - Mireia Bartrons
- Aquatic Ecology Group, University of Vic (UVic-UCC), Catalonia, Spain
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13
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Hu J, Barrett RDH. The role of plastic and evolved DNA methylation in parallel adaptation of threespine stickleback (Gasterosteus aculeatus). Mol Ecol 2022; 32:1581-1591. [PMID: 36560898 DOI: 10.1111/mec.16832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Repeated phenotypic patterns among populations undergoing parallel evolution in similar environments provide support for the deterministic role of natural selection. Epigenetic modifications can mediate plastic and evolved phenotypic responses to environmental change and might make important contributions to parallel adaptation. While many studies have explored the genetic basis of repeated phenotypic divergence, the role of epigenetic processes during parallel adaptation remains unclear. The parallel evolution of freshwater ecotypes of threespine stickleback fish (Gasterosteus aculeatus) following colonization of thousands of lakes and streams from the ocean is a classic example of parallel phenotypic and genotypic adaptation. To investigate epigenetic modifications during parallel adaptation of threespine stickleback, we reanalysed three independent data sets that investigated DNA methylation variation between marine and freshwater ecotypes. Although we found widespread methylation differentiation between ecotypes, there was no significant tendency for CpG sites associated with repeated methylation differentiation across studies to be parallel versus nonparallel. To next investigate the role of plastic versus evolved changes in methylation during freshwater adaptation, we explored if CpG sites exhibiting methylation plasticity during salinity change were more likely to also show evolutionary divergence in methylation between ecotypes. The directions of divergence between ecotypes were generally in the opposite direction to those observed for plasticity when ecotypes were challenged with non-native salinity conditions, suggesting that most plastic responses are likely to be maladaptive during colonization of new environments. Finally, we found a greater number of CpG sites showing evolved changes when ancestral marine ecotypes are acclimated to freshwater environments, whereas plastic changes predominate when derived freshwater ecotypes transition back to their ancestral marine environments. These findings provide evidence for an epigenetic contribution to parallel adaptation and demonstrate the contrasting roles of plastic and evolved methylation differences during adaptation to new environments.
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Affiliation(s)
- Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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14
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Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
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15
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Konečná V, Šustr M, Požárová D, Čertner M, Krejčová A, Tylová E, Kolář F. Genomic basis and phenotypic manifestation of (non-)parallel serpentine adaptation in Arabidopsis arenosa. Evolution 2022; 76:2315-2331. [PMID: 35950324 DOI: 10.1111/evo.14593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.
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Affiliation(s)
- Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Marek Šustr
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Anna Krejčová
- Faculty of Chemical Technology, University of Pardubice, Pardubice, 532 10, Czech Republic
| | - Edita Tylová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 128 00, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, 128 00, Czech Republic.,Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
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16
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Ishikawa A, Yamanouchi S, Iwasaki W, Kitano J. Convergent copy number increase of genes associated with freshwater colonization in fishes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200509. [PMID: 35634928 PMCID: PMC9149799 DOI: 10.1098/rstb.2020.0509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/14/2022] [Indexed: 07/20/2023] Open
Abstract
Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB8a) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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17
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Aguirre WE, Reid K, Rivera J, Heins DC, Veeramah KR, Bell MA. Freshwater Colonization, Adaptation, and Genomic Divergence in Threespine Stickleback. Integr Comp Biol 2022; 62:388-405. [PMID: 35660873 PMCID: PMC9405723 DOI: 10.1093/icb/icac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/25/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
The Threespine Stickleback is ancestrally a marine fish, but many marine populations breed in fresh water (i.e., are anadromous), facilitating their colonization of isolated freshwater habitats a few years after they form. Repeated adaptation to fresh water during at least 10 My and continuing today has led to Threespine Stickleback becoming a premier system to study rapid adaptation. Anadromous and freshwater stickleback breed in sympatry and may hybridize, resulting in introgression of freshwater-adaptive alleles into anadromous populations, where they are maintained at low frequencies as ancient standing genetic variation. Anadromous stickleback have accumulated hundreds of freshwater-adaptive alleles that are disbursed as few loci per marine individual and provide the basis for adaptation when they colonize fresh water. Recent whole-lake experiments in lakes around Cook Inlet, Alaska have revealed how astonishingly rapid and repeatable this process is, with the frequency of 40% of the identified freshwater-adaptive alleles increasing from negligible (∼1%) in the marine founder to ≥50% within ten generations in fresh water, and freshwater phenotypes evolving accordingly. These high rates of genomic and phenotypic evolution imply very intense directional selection on phenotypes of heterozygotes. Sexual recombination rapidly assembles freshwater-adaptive alleles that originated in different founders into multilocus freshwater haplotypes, and regions important for adaptation to freshwater have suppressed recombination that keeps advantageous alleles linked within large haploblocks. These large haploblocks are also older and appear to have accumulated linked advantageous mutations. The contemporary evolution of Threespine Stickleback has provided broadly applicable insights into the mechanisms that facilitate rapid adaptation.
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Affiliation(s)
- Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614, USA
| | - Kerry Reid
- School of Biological Sciences, Area of Ecology and Biodiversity, University of Hong Kong, Hong Kong, SAR, China.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jessica Rivera
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans 70118, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720, USA
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18
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution 2022; 76:1301-1319. [PMID: 35398888 PMCID: PMC9320971 DOI: 10.1111/evo.14490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 01/21/2023]
Abstract
In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.
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Affiliation(s)
- David A. Marques
- Department of BiologyUniversity of VictoriaVictoriaBCV8W 3N5Canada,Aquatic Ecology and Evolution, Institute of Ecology and EvolutionUniversity of BernBernCH‐3012Switzerland,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (EAWAG), Eawag ‐ Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumCH‐6047Switzerland,Natural History Museum BaselBaselCH‐4051Switzerland
| | - Felicity C. Jones
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA,Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA,Friedrich Miescher Laboratory of the Max Planck SocietyTübingen72076Germany
| | - Federica Di Palma
- Earlham InstituteNorwichNR4 7UZUnited Kingdom,Department of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUnited Kingdom
| | - David M. Kingsley
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA,Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA
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19
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Bracamonte SE, Hofmann MJ, Lozano-Martín C, Eizaguirre C, Barluenga M. Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex. BMC Ecol Evol 2022; 22:41. [PMID: 35365100 PMCID: PMC8974093 DOI: 10.1186/s12862-022-01997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
Background Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation. Results We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes. Conclusions Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01997-9.
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Affiliation(s)
- Seraina E Bracamonte
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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20
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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21
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Dahms C, Kemppainen P, Zanella LN, Zanella D, Carosi A, Merilä J, Momigliano P. Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks. Mol Ecol 2021; 31:1234-1253. [PMID: 34843145 DOI: 10.1111/mec.16295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b-RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average FST ≈ 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine-freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.
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Affiliation(s)
- Carolin Dahms
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Linda N Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Davor Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Perugia, Italy
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division for Ecology and Biodiversity, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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22
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Haenel Q, Guerard L, MacColl ADC, Berner D. The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish. Mol Ecol 2021; 31:811-821. [PMID: 34753205 PMCID: PMC9299253 DOI: 10.1111/mec.16269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long‐term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat—nutrient‐depleted acidic lakes—based on whole‐genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic‐adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds.
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Affiliation(s)
- Quiterie Haenel
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Laurent Guerard
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | | | - Daniel Berner
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Weber AAT, Rajkov J, Smailus K, Egger B, Salzburger W. Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes. SCIENCE ADVANCES 2021; 7:eabg5391. [PMID: 34731007 PMCID: PMC8565912 DOI: 10.1126/sciadv.abg5391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.
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McCulloch GA, Guhlin J, Dutoit L, Harrop TWR, Dearden PK, Waters JM. Genomic signatures of parallel alpine adaptation in recently evolved flightless insects. Mol Ecol 2021; 30:6677-6686. [PMID: 34592029 DOI: 10.1111/mec.16204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 12/01/2022]
Abstract
Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low-elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome-wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within-stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing-development (e.g., dishevelled), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo) and lifespan (e.g., Mrp4), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes (hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation.
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Affiliation(s)
| | - Joseph Guhlin
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Thomas W R Harrop
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Waters JM, McCulloch GA. Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution. Mol Ecol 2021; 30:4162-4172. [PMID: 34133810 DOI: 10.1111/mec.16018] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022]
Abstract
Biologists have long been intrigued by apparently predictable and repetitive evolutionary trajectories inferred across a variety of lineages and systems. In recent years, high-throughput sequencing analyses have started to transform our understanding of such repetitive shifts. While researchers have traditionally categorized such shifts as either "convergent" or "parallel," based on relatedness of the lineages involved, emerging genomic insights provide an opportunity to better describe the actual evolutionary mechanisms at play. A synthesis of recent genomic analyses confirms that convergence is the predominant driver of repetitive evolution among species, whereas repeated sorting of standing variation is the major driver of repeated shifts within species. However, emerging data reveal numerous notable exceptions to these expectations, with recent examples of de novo mutations underpinning convergent shifts among even very closely related lineages, while repetitive sorting processes have occurred among even deeply divergent taxa, sometimes via introgression. A number of very recent analyses have found evidence for both processes occurring on different scales within taxa. We suggest that the relative importance of convergent versus sorting processes depends on the interplay between gene flow among populations, and phylogenetic relatedness of the lineages involved.
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Fang B, Kemppainen P, Momigliano P, Merilä J. Population structure limits parallel evolution in sticklebacks. Mol Biol Evol 2021; 38:4205-4221. [PMID: 33956140 PMCID: PMC8476136 DOI: 10.1093/molbev/msab144] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland.,Research Division of Ecology and Biodiversity, Faculty of Science, Kadoorie Building, The University of Hong Kong, Hong Kong SAR
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Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA. Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies. PLoS Genet 2021; 17:e1009566. [PMID: 34029313 PMCID: PMC8177651 DOI: 10.1371/journal.pgen.1009566] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/04/2021] [Accepted: 04/27/2021] [Indexed: 01/21/2023] Open
Abstract
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
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Affiliation(s)
- James R. Whiting
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Paul J. Parsons
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bonnie A. Fraser
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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