1
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Yi X, Kemppainen P, Merilä J. SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering. Mol Ecol Resour 2024:e13985. [PMID: 38850116 DOI: 10.1111/1755-0998.13985] [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: 03/19/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024]
Abstract
Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.
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Affiliation(s)
- Xueling Yi
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Petri Kemppainen
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, Helsinki, Finland
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2
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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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3
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Kess T, Lehnert SJ, Bentzen P, Duffy S, Messmer A, Dempson JB, Newport J, Whidden C, Robertson MJ, Chaput G, Breau C, April J, Gillis C, Kent M, Nugent CM, Bradbury IR. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon. Ecol Evol 2024; 14:e11068. [PMID: 38584771 PMCID: PMC10995719 DOI: 10.1002/ece3.11068] [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: 01/06/2024] [Accepted: 01/31/2024] [Indexed: 04/09/2024] Open
Abstract
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large single-nucleotide polymorphism (SNP) array and low-coverage whole-genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large-effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.
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Affiliation(s)
- Tony Kess
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Steven Duffy
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Amber Messmer
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - J. Brian Dempson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Jason Newport
- Marine Environmental Research Infrastructure for Data Integration and Application NetworkHalifaxNova ScotiaCanada
| | | | - Martha J. Robertson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Gerald Chaput
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Cindy Breau
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Julien April
- Ministère des Forêts de la Faune et des ParcsQuebecQuebecCanada
| | - Carole‐Anne Gillis
- Gespe'gewa'gi, Mi'gma'qi, ListugujGespe'gewa'gi Institute of Natural UnderstandingQuebecQuebecCanada
| | - Matthew Kent
- Centre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Cameron M. Nugent
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
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4
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Fraimout A, Guillaume F, Li Z, Sillanpää MJ, Rastas P, Merilä J. Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing. Mol Ecol 2024; 33:e17299. [PMID: 38380534 DOI: 10.1111/mec.17299] [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: 07/28/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which, in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogeneous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.
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Affiliation(s)
- Antoine Fraimout
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Frédéric Guillaume
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Zitong Li
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mikko J Sillanpää
- Research Unit of Mathematical Sciences, FI-90014 University of Oulu, Oulu, Finland
| | - Pasi Rastas
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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5
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Medina I, Dong C, Marquez R, Perez DM, Wang IJ, Stuart-Fox D. Anti-predator defences are linked with high levels of genetic differentiation in frogs. Proc Biol Sci 2024; 291:20232292. [PMID: 38264783 PMCID: PMC10806439 DOI: 10.1098/rspb.2023.2292] [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: 01/15/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.
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Affiliation(s)
- Iliana Medina
- School of BioSciences, University of Melbourne, Melbourne 3010, Australia
| | - Caroline Dong
- School of BioSciences, University of Melbourne, Melbourne 3010, Australia
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70115, USA
| | - Roberto Marquez
- Department of Ecology and Evolutionary Biology and Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniela M. Perez
- Max Plank Institute of Animal Behaviour, 78464 Konstanz, Germany
| | - Ian J. Wang
- Department of Environmental Science, Policy, and Management, Rausser College of Natural Resources, University of California, Berkeley, CA 94720, USA
| | - Devi Stuart-Fox
- School of BioSciences, University of Melbourne, Melbourne 3010, Australia
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6
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Rosing-Asvid A, Löytynoja A, Momigliano P, Hansen RG, Scharff-Olsen CH, Valtonen M, Kammonen J, Dietz R, Rigét FF, Ferguson SH, Lydersen C, Kovacs KM, Holland DM, Jernvall J, Auvinen P, Tange Olsen M. An evolutionarily distinct ringed seal in the Ilulissat Icefjord. Mol Ecol 2023; 32:5932-5943. [PMID: 37855154 DOI: 10.1111/mec.17163] [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: 06/26/2023] [Revised: 09/20/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The Earth's polar regions are low rates of inter- and intraspecific diversification. An extreme mammalian example is the Arctic ringed seal (Pusa hispida hispida), which is assumed to be panmictic across its circumpolar Arctic range. Yet, local Inuit communities in Greenland and Canada recognize several regional variants; a finding supported by scientific studies of body size variation. It is however unclear whether this phenotypic variation reflects plasticity, morphs or distinct ecotypes. Here, we combine genomic, biologging and survey data, to document the existence of a unique ringed seal ecotype in the Ilulissat Icefjord (locally 'Kangia'), Greenland; a UNESCO World Heritage site, which is home to the most productive marine-terminating glacier in the Arctic. Genomic analyses reveal a divergence of Kangia ringed seals from other Arctic ringed seals about 240 kya, followed by secondary contact since the Last Glacial Maximum. Despite ongoing gene flow, multiple genomic regions appear under strong selection in Kangia ringed seals, including candidate genes associated with pelage coloration, growth and osmoregulation, potentially explaining the Kangia seal's phenotypic and behavioural uniqueness. The description of 'hidden' diversity and adaptations in yet another Arctic species merits a reassessment of the evolutionary processes that have shaped Arctic diversity and the traditional view of this region as an evolutionary freezer. Our study highlights the value of indigenous knowledge in guiding science and calls for efforts to identify distinct populations or ecotypes to understand how these might respond differently to environmental change.
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Affiliation(s)
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Paolo Momigliano
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, Spain
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | | | - Mia Valtonen
- Wildlife Ecology Group, Natural Resources Institute Finland, Helsinki, Finland
| | - Juhana Kammonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Rune Dietz
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | | | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, Tromsø, Norway
| | - David M Holland
- Mathematics and Atmosphere/Ocean Science, Courant Institute of Mathematical Sciences, New York University, New York City, New York, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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7
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Shankregowda AM, Siriyappagouder P, Kuizenga M, Bal TMP, Abdelhafiz Y, Eizaguirre C, Fernandes JMO, Kiron V, Raeymaekers JAM. Host habitat rather than evolutionary history explains gut microbiome diversity in sympatric stickleback species. Front Microbiol 2023; 14:1232358. [PMID: 37901806 PMCID: PMC10601471 DOI: 10.3389/fmicb.2023.1232358] [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: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Host-associated microbiota can influence host phenotypic variation, fitness and potential to adapt to local environmental conditions. In turn, both host evolutionary history and the abiotic and biotic environment can influence the diversity and composition of microbiota. Yet, to what extent environmental and host-specific factors drive microbial diversity remains largely unknown, limiting our understanding of host-microbiome interactions in natural populations. Here, we compared the intestinal microbiota between two phylogenetically related fishes, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) in a common landscape. Using amplicon sequencing of the V3-V4 region of the bacterial 16S rRNA gene, we characterised the α and β diversity of the microbial communities in these two fish species from both brackish water and freshwater habitats. Across eight locations, α diversity was higher in the nine-spined stickleback, suggesting a broader niche use in this host species. Habitat was a strong determinant of β diversity in both host species, while host species only explained a small fraction of the variation in gut microbial composition. Strong habitat-specific effects overruled effects of geographic distance and historical freshwater colonisation, suggesting that the gut microbiome correlates primarily with local environmental conditions. Interestingly, the effect of habitat divergence on gut microbial communities was stronger in three-spined stickleback than in nine-spined stickleback, possibly mirroring the stronger level of adaptive divergence in this host species. Overall, our results show that microbial communities reflect habitat divergence rather than colonisation history or dispersal limitation of host species.
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Affiliation(s)
| | | | - Marijn Kuizenga
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | | | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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8
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Zhang C, Reid K, Sands AF, Fraimout A, Schierup MH, Merilä J. De Novo Mutation Rates in Sticklebacks. Mol Biol Evol 2023; 40:msad192. [PMID: 37648662 PMCID: PMC10503787 DOI: 10.1093/molbev/msad192] [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: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.
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Affiliation(s)
- Chaowei Zhang
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Kerry Reid
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Arthur F Sands
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Antoine Fraimout
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Research Program in Organismal & Evolutionary Biology, Faculty Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Juha Merilä
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Research Program in Organismal & Evolutionary Biology, Faculty Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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9
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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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10
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Yamaguchi R, Wiley B, Otto SP. The phoenix hypothesis of speciation. Proc Biol Sci 2022; 289:20221186. [PMID: 36382528 PMCID: PMC9667362 DOI: 10.1098/rspb.2022.1186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2023] Open
Abstract
Genetic divergence among allopatric populations builds reproductive isolation over time. This process is accelerated when populations face a changing environment that allows large-effect mutational differences to accumulate, but abrupt change also places populations at risk of extinction. Here we use simulations of Fisher's geometric model with explicit population dynamics to explore the genetic changes that occur in the face of environmental changes. Because evolutionary rescue leads to the fixation of mutations whose phenotypic effects are larger on average compared with populations not at risk of extinction, these mutations are thus more likely to lead to reproductive isolation. We refer to the formation of new species from the ashes of populations in decline as the phoenix hypothesis of speciation. The phoenix hypothesis predicts more substantial hybrid fitness breakdown among populations surviving a higher extinction risk. The hypothesis was supported when many loci underlie adaptation. With only a small number of potential rescue mutations, however, mutations that fixed in different populations were more likely to be identical, with such parallel changes reducing isolation. Consequently, reproductive isolation builds fastest in populations subject to an intermediate extinction risk, given a limited number of mutations available for adaptation.
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Affiliation(s)
- Ryo Yamaguchi
- Department of Advanced Transdisciplinary Science, Hokkaido University, Sapporo, Hokkaido 060-0808, Japan
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Bryn Wiley
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Sarah P. Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
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11
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Fraimout A, Päiviö E, Merilä J. Relaxed risk of predation drives parallel evolution of stickleback behavior. Evolution 2022; 76:2712-2723. [PMID: 36117280 PMCID: PMC9827860 DOI: 10.1111/evo.14631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/14/2022] [Accepted: 07/26/2022] [Indexed: 01/22/2023]
Abstract
The occurrence of similar phenotypes in multiple independent populations derived from common ancestral conditions (viz. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (Pungitius pungitius) likely explains the divergence in complex behaviors between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioral traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that divergence in behavior between habitats is aligned with the response to relaxation of predation pressure. Finally, we show alignment across multiple pairs of populations, and that relaxation of predation pressure has likely driven parallel evolution of behavior in this species.
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Affiliation(s)
- Antoine Fraimout
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland,Area of Ecology and Biodiversity, School of Biological SciencesThe University of Hong KongHong Kong SAR
| | - Elisa Päiviö
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki00014Finland,Area of Ecology and Biodiversity, School of Biological SciencesThe University of Hong KongHong Kong SAR
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12
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Yang F, Crossley MS, Schrader L, Dubovskiy IM, Wei SJ, Zhang R. Polygenic adaptation contributes to the invasive success of the Colorado potato beetle. Mol Ecol 2022; 31:5568-5580. [PMID: 35984732 DOI: 10.1111/mec.16666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 07/03/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
How invasive species cope with novel selective pressures with limited genetic variation is a fundamental question in molecular ecology. Several mechanisms have been proposed, but they can lack generality. Here, we addressed an alternative solution, polygenic adaptation, wherein traits that arise from multiple combinations of loci may be less sensitive to loss of variation during invasion. We tested the polygenic signal of environmental adaptation of Colorado potato beetle (CPB) introduced in Eurasia. Population genomic analyses showed declining genetic diversity in the eastward expansion of Eurasian populations, and weak population genetic structure (except for the invasion fronts in Asia). Demographic history showed that all populations shared a strong bottleneck about 100 years ago when CPB was introduced to Europe. Genome scans revealed a suite of genes involved in activity regulation functions that are plausibly related to cold stress, including some well-founded functions (e.g., the activity of phosphodiesterase, the G-protein regulator) and discrete functions. Such polygenic architecture supports the hypothesis that polygenic adaptation and potentially genetic redundancy can fuel the adaptation of CPB despite strong genetic depletion, thus representing a promising general mechanism for resolving the genetic paradox of invasion. More broadly, most complex traits based on polygenes may be less sensitive to invasive bottlenecks, thus ensuring the evolutionary success of invasive species in novel environments.
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Affiliation(s)
- Fangyuan Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Beijing Academy of Agriculture and Forestry Sciences, Institute of Plant and Environmental Protection, Beijing, China
| | - Michael S Crossley
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, USA
| | - Lukas Schrader
- Institute for Evolution & Biodiversity, University of Münster, Münster, Germany
| | - Ivan M Dubovskiy
- Laboratory of Biological Plant Protection and Biotechnology, Novosibirsk State Agrarian University, Novosibirsk, Russia
| | - Shu-Jun Wei
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Plant and Environmental Protection, Beijing, China
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
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13
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Nedoluzhko A, Orlova SY, Kurnosov DS, Orlov AM, Galindo-Villegas J, Rastorguev SM. Genomic Signatures of Freshwater Adaptation in Pacific Herring ( Clupea pallasii). Genes (Basel) 2022; 13:genes13101856. [PMID: 36292743 PMCID: PMC9601299 DOI: 10.3390/genes13101856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 107140 Moscow, Russia
- Laboratory of Genetic Basis of Identification, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Denis S. Kurnosov
- Research Group of Intraspecific Differentiation, Russian Federal Research Institute of Fisheries and Oceanography, Pacific Branch (TINRO), 690091 Vladivostok, Russia
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
- Department of Ichthyology and Hydrobiology, Tomsk State University, 634050 Tomsk, Russia
- Laboratory of Marine Biology, Caspian Institute of Biological Resources, Russian Academy of Sciences, 367000 Makhachkala, Russia
| | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Sergey M. Rastorguev
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
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14
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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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15
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Whiting JR, Paris JR, van der Zee MJ, Fraser BA. AF‐vapeR
: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James R. Whiting
- Department of Biosciences University of Exeter Exeter UK
- Department of Biological Sciences University of Calgary Calgary Alberta Canada
| | - Josephine R. Paris
- Department of Biosciences University of Exeter Exeter UK
- Department of Health, Life and Environmental Sciences University of L'Aquila L'Aquila Italy
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16
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Fang B, Momigliano P, Kahilainen KK, Merilä J. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 2022; 76:1905-1913. [PMID: 35797649 DOI: 10.1111/evo.14559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, 36310, Spain
| | - Kimmo K Kahilainen
- Lammi Biological Station, University of Helsinki, Lammi, 16900, Finland.,Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, 99490, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
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17
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Population Structure and Genetic Diversity of Chinese Honeybee (Apis Cerana Cerana) in Central China. Genes (Basel) 2022; 13:genes13061007. [PMID: 35741769 PMCID: PMC9222672 DOI: 10.3390/genes13061007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 12/22/2022] Open
Abstract
Central China has a rich terrain with a temperate monsoon climate and varied natural environments for the Chinese honeybee (Apis cerana cerana). However, little comprehensive research on population genetic diversity has been done in this area. A population survey of the structure and genetic diversity of Apis cerana cerana in this area is deeply needed for understanding adaptation to variable environments and providing more references for the protection of honeybee biodiversity. In this study, we present a dataset of 72 populations of Chinese honeybees collected from nine sites by whole genome sequencing in Central China. We obtained 2,790,214,878 clean reads with an average covering a depth of 22×. A total of 27,361,052 single nucleotide polymorphisms (SNPs) were obtained by mapping to the reference genome with an average mapping rate of 93.03%. Genetic evolution analysis was presented via the population structure and genetic diversity based on the datasets of SNPs. It showed that Apis cerana cerana in plains exhibited higher genetic diversity than in mountain areas. The mantel test between Apis cerana cerana groups revealed that some physical obstacles, especially the overurbanization of the plains, contributed to the differentiation. This study is conducive to elucidating the evolution of Apis cerana in different environments and provides a theoretical basis for investigating and protecting the Chinese honeybee.
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18
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Fraimout A, Li Z, Sillanpää MJ, Merilä J. Age-dependent genetic architecture across ontogeny of body size in sticklebacks. Proc Biol Sci 2022; 289:20220352. [PMID: 35582807 PMCID: PMC9118060 DOI: 10.1098/rspb.2022.0352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Heritable variation in traits under natural selection is a prerequisite for evolutionary response. While it is recognized that trait heritability may vary spatially and temporally depending on which environmental conditions traits are expressed under, less is known about the possibility that genetic variance contributing to the expected selection response in a given trait may vary at different stages of ontogeny. Specifically, whether different loci underlie the expression of a trait throughout development and thus providing an additional source of variation for selection to act on in the wild, is unclear. Here we show that body size, an important life-history trait, is heritable throughout ontogeny in the nine-spined stickleback (Pungitius pungitius). Nevertheless, both analyses of quantitative trait loci and genetic correlations across ages show that different chromosomes/loci contribute to this heritability in different ontogenic time-points. This suggests that body size can respond to selection at different stages of ontogeny but that this response is determined by different loci at different points of development. Hence, our study provides important results regarding our understanding of the genetics of ontogeny and opens an interesting avenue of research for studying age-specific genetic architecture as a source of non-parallel evolution.
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Affiliation(s)
- Antoine Fraimout
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014, Finland
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014, Finland.,CSIRO Agriculture and Food, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Mikko J Sillanpää
- Research Unit of Mathematical Sciences, University of Oulu, FI-90014, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014, Finland.,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR
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19
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Sabatino SJ, Pereira P, Carneiro M, Dilytė J, Archer JP, Munoz A, Nonnis-Marzano F, Murias A. The genetics of adaptation in freshwater Eurasian shad ( Alosa). Ecol Evol 2022; 12:e8908. [PMID: 35646309 PMCID: PMC9130566 DOI: 10.1002/ece3.8908] [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: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
Studying the genetics of phenotypic convergence can yield important insights into adaptive evolution. Here, we conducted a comparative genomic study of four lineages (species and subspecies) of anadromous shad (Alosa) that have independently evolved life cycles entirely completed in freshwater. Three naturally diverged (A. fallax lacustris, A. f. killarnensis, and A. macedonica), and the fourth (A. alosa) was artificially landlocked during the last century. To conduct this analysis, we assembled and annotated a draft of the A. alosa genome and generated whole‐genome sequencing for 16 anadromous and freshwater populations of shad. Widespread evidence for parallel genetic changes in freshwater populations within lineages was found. In freshwater A. alosa, which have only been diverging for tens of generations, this shows that parallel adaptive evolution can rapidly occur. However, parallel genetic changes across lineages were comparatively rare. The degree of genetic parallelism was not strongly related to the number of shared polymorphisms between lineages, thus suggesting that other factors such as divergence among ancestral populations or environmental variation may influence genetic parallelism across these lineages. These overall patterns were exemplified by genetic differentiation involving a paralog of ATPase‐α1 that appears to be under selection in just two of the more distantly related lineages studied, A. f. lacustris and A. alosa. Our findings provide insights into the genetic architecture of adaptation and parallel evolution along a continuum of population divergence.
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Affiliation(s)
- Stephen J Sabatino
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Paulo Pereira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Miguel Carneiro
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Jolita Dilytė
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
| | - John Patrick Archer
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
| | - Antonio Munoz
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal
| | - Francesco Nonnis-Marzano
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal.,Department of Chemistry, Life Sciences and Environmental Sustainability Università di Parma Parma Italy
| | - Antonio Murias
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal.,BIOPOLIS - Program in Genomics, Biodiversity and Land Planning CIBIO Vairão Portugal.,Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
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20
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Guzmán NV, Kemppainen P, Monti D, Castillo ERD, Rodriguero MS, Sánchez-Restrepo AF, Cigliano MM, Confalonieri VA. Stable inversion clines in a grasshopper species group despite complex geographical history. Mol Ecol 2021; 31:1196-1215. [PMID: 34862997 DOI: 10.1111/mec.16305] [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: 05/21/2020] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
Chromosomal inversions are known to play roles in adaptation and differentiation in many species. They involve clusters of correlated genes (i.e., loci in linkage disequilibrium, LD) possibly associated with environmental variables. The grasshopper "species complex" Trimerotropis pallidipennis comprises several genetic lineages distributed from North to South America in arid and semi-arid high-altitude environments. The southernmost lineage, Trimerotropis sp., segregates for four to seven putative inversions that display clinal variation, possibly through adaptation to temperate environments. We analysed chromosomal, mitochondrial and genome-wide single nucleotide polymorphism data in 19 Trimerotropis sp. populations mainly distributed along two altitudinal gradients (MS and Ju). Populations across Argentina comprise two main chromosomally and genetically differentiated lineages: one distributed across the southernmost border of the "Andes Centrales," adding evidence for a differentiation hotspot in this area; and the other widely distributed in Argentina. Within the latter, network analytical approaches to LD found three clusters of correlated loci (LD-clusters), with inversion karyotypes explaining >79% of the genetic variation. Outlier loci associated with environmental variables mapped to two of these LD-clusters. Furthermore, despite the complex geographical history indicated by population genetic analyses, the clines in inversion karyotypes have remained stable for more than 20 generations, implicating their role in adaptation and differentiation within this lineage. We hypothesize that these clines could be the consequence of a coupling between extrinsic postzygotic barriers and spatially varying selection along environmental gradients resulting in a hybrid zone. These results provide a framework for future investigations about candidate genes implicated in rapid adaptation to new environments.
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Affiliation(s)
- Noelia V Guzmán
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Daniela Monti
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Elio R D Castillo
- Laboratorio de Genética Evolutiva "Dr. Claudio J. Bidau", FCEQyN, Universidad Nacional de Misiones (UNaM), Instituto de Biología Subtropical (IBS) (CONICET/UNaM), LQH, Posadas, Misiones, Argentina
| | - Marcela S Rodriguero
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Andrés F Sánchez-Restrepo
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina.,Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
| | - Maria Marta Cigliano
- Museo de La Plata, Centro de Estudios Parasitológicos y de Vectores (CEPAVE- CONICET/UNLP), Universidad Nacional de la Plata, Buenos Aires, Argentina
| | - Viviana A Confalonieri
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
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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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Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
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