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Fox JA, Hunt DAGA, Hendry AP, Chapman LJ, Barrett RDH. Counter-gradient variation in gene expression between fish populations facilitates colonization of low-dissolved oxygen environments. Mol Ecol 2024; 33:e17419. [PMID: 38808559 DOI: 10.1111/mec.17419] [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: 11/13/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
The role of phenotypic plasticity during colonization remains unclear due to the shifting importance of plasticity across timescales. In the early stages of colonization, plasticity can facilitate persistence in a novel environment; but over evolutionary time, processes such as genetic assimilation may reduce variation in plastic traits such that species with a longer evolutionary history in an environment can show lower levels of plasticity than recent invaders. Therefore, comparing species in the early stages of colonization to long-established species provides a powerful approach for uncovering the role of phenotypic plasticity during different stages of colonization. We compared gene expression between low-dissolved oxygen (DO) and high-DO populations of two cyprinid fish: Enteromius apleurogramma, a species that has undergone a recent range expansion, and E. neumayeri, a long-established native species in the same region. We sampled tissue either immediately after capture from the field or after a 2-week acclimation under high-DO conditions, allowing us to test for both evolved and plastic differences in low-DO vs high-DO populations of each species. We found that most genes showing candidate-evolved differences in gene expression did not overlap with those showing plastic differences in gene expression. However, in the genes that did overlap, there was counter-gradient variation such that plastic and evolved gene expression responses were in opposite directions in both species. Additionally, E. apleurogramma had higher levels of plasticity and evolved divergence in gene expression between field populations. We suggest that the higher level of plasticity and counter-gradient variation may have allowed rapid genetic adaptation in E. apleurogramma and facilitated colonization. This study shows how counter-gradient variation may impact the colonization of divergent oxygen environments.
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Affiliation(s)
- Janay A Fox
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - David A G A Hunt
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hendry
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
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2
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Geng FD, Liu MQ, Zhang XD, Wang LZ, Lei MF. Genomics of hybrid parallel origin in Aquilegia ecalcarata. BMC Ecol Evol 2024; 24:75. [PMID: 38844857 PMCID: PMC11155106 DOI: 10.1186/s12862-024-02266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear. RESULTS In this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata. CONCLUSIONS Our results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.
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Affiliation(s)
- Fang-Dong Geng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Miao-Qing Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xue-Dong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Lu-Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meng-Fan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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3
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Seuront L, Henry S, Breton E, Spilmont N, Elias F. Marine foams impede metabolic and behavioural traits in the rough periwinkle Littorina saxatilis. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106486. [PMID: 38588615 DOI: 10.1016/j.marenvres.2024.106486] [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: 11/19/2023] [Revised: 03/20/2024] [Accepted: 03/30/2024] [Indexed: 04/10/2024]
Abstract
Foams are a ubiquitous feature of marine environments. They can have major economic, societal and ecological consequences through their accumulation on the shore. Despite their pervasive nature and evidence that stable foam deposits play a pivotal role in the ecology of soft shore and estuaries, very limited amounts of information are available on their contribution to the structure and function at play in rocky intertidal ecosystems. This study shows that the metabolic rate of the high-shore gastropod Littorina saxatilis is significantly higher in individuals exposed to foams. Behavioural assays conducted under laboratory-controlled conditions further show that this species detects foam-born infochemicals both indirectly or directly, hence rely on both airborne and contact chemosensory cues. L. saxatilis also actively avoid areas covered in foam, and increase their activity in the presence of foam. These observations are interpreted in terms of foam-induced increased metabolic stress and increases behavioural anxiety and vigilance. They are further discussed in relation to the occurrence of two phytoplankton species known to produce repellent and/or toxic compounds such as domoic acid and dimethylsulfoniopropionate, the diatom Pseudo-nitzschia multistriata and the haptophyte Phaeocystis globosa, with the latter occurring at unusually high density. Taken together, these results suggest that the accumulation of foams on intertidal rocky shores may have major implications on taxa relying on both airborne and contact chemosensory cues to navigate, find food and mating partners. Specifically, the observed increased behavioural activity coupled with increased metabolic demands may impact species fitness and highlight potentially large ecological consequences in rocky intertidal ecosystems characterized by strong hydrodynamism and elevated organic matter content leading to the presence of long-lived foam.
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Affiliation(s)
- Laurent Seuront
- CNRS, Univ. Lille, Univ. Littoral Côte D'Opale, IRD, UMR 8187 LOG, Station Marine de Wimereux, F-59000, Lille, France; Department of Marine Resources and Energy, Tokyo University of Marine Science and Technology, Tokyo, Japan; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa.
| | - Solène Henry
- CNRS, Univ. Lille, Univ. Littoral Côte D'Opale, IRD, UMR 8187 LOG, Station Marine de Wimereux, F-59000, Lille, France
| | - Elsa Breton
- Univ. Littoral Côte D'Opale, CNRS, Univ. Lille, IRD, UMR 8187 LOG, F-59000, Lille, France
| | - Nicolas Spilmont
- CNRS, Univ. Lille, Univ. Littoral Côte D'Opale, IRD, UMR 8187 LOG, Station Marine de Wimereux, F-59000, Lille, France
| | - Florence Elias
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes, ESPCI-PSL-Sorbonne Université-Université de Paris, 75005, Paris, France
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4
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Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. Diverse pathways to speciation revealed by marine snails. Trends Genet 2024; 40:337-351. [PMID: 38395682 DOI: 10.1016/j.tig.2024.01.002] [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: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024]
Abstract
Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Rui Faria
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Alan Le Moan
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CNRS & Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Marina Rafajlović
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Department of Marine Sciences, University of Gothenburg, SE 41390 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Anja Marie Westram
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Roger K Butlin
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Sean Stankowski
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Institute of Science and Technology Austria, Klosterneuburg, Austria; Department of Ecology and Evolution, University of Sussex, Brighton, UK
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5
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Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Castillo DG, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. The genetic basis of a recent transition to live-bearing in marine snails. Science 2024; 383:114-119. [PMID: 38175895 DOI: 10.1126/science.adi2982] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/25/2023] [Indexed: 01/06/2024]
Abstract
Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer-specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer-specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.
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Affiliation(s)
- Sean Stankowski
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Department of Ecology and Evolution, University of Sussex, Brighton BN1 9RH, UK
| | - Zuzanna B Zagrodzka
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Martin D Garlovsky
- Department of Applied Zoology, Faculty of Biology, Technische Universität Dresden, 01069 Dresden, Germany
| | - Arka Pal
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Daria Shipilina
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Department of Ecology and Genetics, Program of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | | | - Hila Lifchitz
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Alan Le Moan
- CNRS and Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Erica Leder
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - James Reeve
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96 Strömstad, Sweden
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6
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Gafarova E, Kuracji D, Sogomonyan K, Gorokhov I, Polev D, Zubova E, Golikova E, Granovitch A, Maltseva A. Gut Bacteriomes and Ecological Niche Divergence: An Example of Two Cryptic Gastropod Species. BIOLOGY 2023; 12:1521. [PMID: 38132347 PMCID: PMC10740740 DOI: 10.3390/biology12121521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Symbiotic microorganisms may provide their hosts with abilities critical to their occupation of microhabitats. Gut (intestinal) bacterial communities aid animals to digest substrates that are either innutritious or toxic, as well as support their development and physiology. The role of microbial communities associated with sibling species in the hosts' adaptation remains largely unexplored. In this study, we examined the composition and plasticity of the bacteriomes in two sibling intertidal gastropod species, Littorina fabalis and L. obtusata, which are sympatric but differ in microhabitats. We applied 16S rRNA gene metabarcoding and shotgun sequencing to describe associated microbial communities and their spatial and temporal variation. A significant drop in the intestinal bacteriome diversity was revealed during the cold season, which may reflect temperature-related metabolic shifts and changes in snail behavior. Importantly, there were significant interspecies differences in the gut bacteriome composition in summer but not in autumn. The genera Vibrio, Aliivibrio, Moritella and Planktotalea were found to be predominantly associated with L. fabalis, while Granulosicoccus, Octadecabacter, Colwellia, Pseudomonas, Pseudoalteromonas and Maribacter were found to be mostly associated with L. obtusata. Based on these preferential associations, we analyzed the metabolic pathways' enrichment. We hypothesized that the L. obtusata gut bacteriome contributes to decomposing algae and detoxifying polyphenols produced by fucoids. Thus, differences in the sets of associated bacteria may equip their closely phylogenetically related hosts with a unique ability to occupy specific micro-niches.
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Affiliation(s)
- Elizaveta Gafarova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Kuracji
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Karina Sogomonyan
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ivan Gorokhov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Polev
- Department of Epidemiology, St. Petersburg Pasteur Institute, Mira Street 14, 197101 St. Petersburg, Russia;
| | - Ekaterina Zubova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Elena Golikova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Andrey Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Arina Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
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7
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Carvalho J, Morales HE, Faria R, Butlin RK, Sousa VC. Integrating Pool-seq uncertainties into demographic inference. Mol Ecol Resour 2023; 23:1737-1755. [PMID: 37475177 DOI: 10.1111/1755-0998.13834] [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: 12/02/2022] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.
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Affiliation(s)
- João Carvalho
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Faria
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Vítor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
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8
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James ME, Allsopp RN, Groh JS, Kaur A, Wilkinson MJ, Ortiz-Barrientos D. Uncovering the genetic architecture of parallel evolution. Mol Ecol 2023; 32:5575-5589. [PMID: 37740681 DOI: 10.1111/mec.17134] [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: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/25/2023]
Abstract
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Robin N Allsopp
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Avneet Kaur
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia
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9
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Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
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Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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10
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Mittermayer F, Helmerson C, Duvetorp M, Johannesson K, Panova M. The molecular background of the aspartate aminotransferase polymorphism in Littorina snails maintained by strong selection on small spatial scales. Gene 2023:147517. [PMID: 37257792 DOI: 10.1016/j.gene.2023.147517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Allozymes present several classical examples of divergent selection, including the variation in the cytosolic aspartate aminotransferase (AAT) in the intertidal snails Littorina saxatilis. AAT is a part of the asparate-malate shuttle, in the interidal molluscs involved in the anaerobic respiration during desiccation. Previous allozyme studies reported the sharp gradient in the frequencies of the AAT100and the AAT120 alleles between the low and high shores in the Northern Europe and the differences in their enzymatic activity, supporting the role of AAT in adaptation to desiccation. However, the populations in the Iberian Peninsula showed the opposite allele cline. Using the mRNA sequencing and the genome pool-seq analyses we characterize DNA sequences of the different AAT alleles, report the amino acid replacements behind the allozyme variation and show that same allozyme alleles in Northern and Southern populations have different protein sequences. Gene phylogeny reveals that the AAT100 and the northern AAT120 alleles represent the old polymorphism, shared among the closely related species of Littorina, while the southern AAT120 allele is more recently derived from AAT100. Further, we show that the Aat gene is expressed at constitutive level in different genotypes and conditions, supporting the role of structural variation in regulation of enzyme activity. Finally, we report the location and the structure of the gene in the L. saxatilis genome and the presence of two additional non-functional gene copies. Altogether, we provide a missing link between the classical allozyme studies and the genome scans and bring together the results produced over decades of the genetic research.
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Affiliation(s)
- Felix Mittermayer
- Research Division Marine Ecology, Research Unit Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany; Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Cecilia Helmerson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo; Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Mårten Duvetorp
- Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden
| | - Marina Panova
- Department of Marine Sciences, University of Gothenburg, Tjärnö, 45296 Strömstad, Sweden.
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11
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Dwane C, Rezende EL, Tills O, Galindo J, Rolán-Alvarez E, Rundle S, Truebano M. Thermodynamic effects drive countergradient responses in the thermal performance of Littorina saxatilis across latitude. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160877. [PMID: 36521622 DOI: 10.1016/j.scitotenv.2022.160877] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Thermal performance curves (TPCs) provide a powerful framework to assess the evolution of thermal sensitivity in populations exposed to divergent selection regimes across latitude. However, there is a lack of consensus regarding the extent to which physiological adjustments that compensate for latitudinal temperature variation (metabolic cold adaptation; MCA) may alter the shape of TPCs, including potential repercussion on upper thermal limits. To address this, we compared TPCs for cardiac activity in latitudinally-separated populations of the intertidal periwinkle Littorina saxatilis. We applied a non-linear TPC modelling approach to explore how different metrics governing the shape of TPCs varied systematically in response to local adaptation and thermal acclimation. Both critical upper limits, and the temperatures at which cardiac performance was maximised, were higher in the northernmost (cold-adapted) population and displayed a countergradient latitudinal trend which was most pronounced following acclimation to low temperatures. We interpret this response as a knock-on consequence of increased standard metabolic rate in high latitude populations, indicating that physiological compensation associated with MCA may indirectly influence variation in upper thermal limits across latitude. Our study highlights the danger of assuming that variation in any one aspect of the TPC is adaptive without appropriate mechanistic and ecological context.
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Affiliation(s)
- Christopher Dwane
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK.
| | - Enrico L Rezende
- Departamento de Ecología, Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 6513677, Chile
| | - Oliver Tills
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Juan Galindo
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Bioquímica, Genética e Inmunología, 36310 Vigo, Spain
| | - Emilio Rolán-Alvarez
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Bioquímica, Genética e Inmunología, 36310 Vigo, Spain
| | - Simon Rundle
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
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12
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Life on a beach leads to phenotypic divergence despite gene flow for an island lizard. Commun Biol 2023; 6:141. [PMID: 36732444 PMCID: PMC9895042 DOI: 10.1038/s42003-023-04494-x] [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: 07/18/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Limited spatial separation within small islands suggests that observed population divergence may occur due to habitat differences without interruption to gene flow but strong evidence of this is scarce. The wall lizard Teira dugesii lives in starkly contrasting shingle beach and inland habitats on the island of Madeira. We used a matched pairs sampling design to examine morphological and genomic divergence between four beach and adjacent (<1 km) inland areas. Beach populations are significantly darker than corresponding inland populations. Geometric morphometric analyses reveal divergence in head morphology: beach lizards have generally wider snouts. Genotyping-by-sequencing allows the rejection of the hypothesis that beach populations form a distinct lineage. Bayesian analyses provide strong support for models that incorporate gene flow, relative to those that do not, replicated at all pairs of matched sites. Madeiran lizards show morphological divergence between habitats in the face of gene flow, revealing how divergence may originate within small islands.
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13
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Johannesson K, Leder EH, André C, Dupont S, Eriksson SP, Harding K, Havenhand JN, Jahnke M, Jonsson PR, Kvarnemo C, Pavia H, Rafajlović M, Rödström EM, Thorndyke M, Blomberg A. Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative. Evol Appl 2023; 16:530-541. [PMID: 36793681 PMCID: PMC9923476 DOI: 10.1111/eva.13389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/08/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
The Centre for Marine Evolutionary Biology (CeMEB) at the University of Gothenburg, Sweden, was established in 2008 through a 10-year research grant of 8.7 m€ to a team of senior researchers. Today, CeMEB members have contributed >500 scientific publications, 30 PhD theses and have organised 75 meetings and courses, including 18 three-day meetings and four conferences. What are the footprints of CeMEB, and how will the centre continue to play a national and international role as an important node of marine evolutionary research? In this perspective article, we first look back over the 10 years of CeMEB activities and briefly survey some of the many achievements of CeMEB. We furthermore compare the initial goals, as formulated in the grant application, with what has been achieved, and discuss challenges and milestones along the way. Finally, we bring forward some general lessons that can be learnt from a research funding of this type, and we also look ahead, discussing how CeMEB's achievements and lessons can be used as a springboard to the future of marine evolutionary biology.
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Affiliation(s)
- Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Erica H Leder
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden.,Natural History Museum University of Oslo Oslo Norway
| | - Carl André
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Sam Dupont
- Department of Biology and Environmental Science University of Gothenburg, Kristineberg Marine Research Station Fiskebäckskil Sweden.,International Atomic Energy Agency Principality of Monaco Monaco
| | - Susanne P Eriksson
- Department of Biology and Environmental Science University of Gothenburg, Kristineberg Marine Research Station Fiskebäckskil Sweden
| | - Karin Harding
- Department of Biology and Environmental Science University of Gothenburg Gothenburg Sweden
| | - Jonathan N Havenhand
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Marlene Jahnke
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Per R Jonsson
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Charlotta Kvarnemo
- Department of Biology and Environmental Science University of Gothenburg Gothenburg Sweden
| | - Henrik Pavia
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Marina Rafajlović
- Department of Marine Sciences University of Gothenburg Gothenburg Sweden
| | - Eva Marie Rödström
- Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - Michael Thorndyke
- Department of Biology and Environmental Science University of Gothenburg, Kristineberg Marine Research Station Fiskebäckskil Sweden.,Department of Genomics Research in Ecology & Evolution in Nature (GREEN) Groningen Institute for Evolutionary Life Sciences (GELIFES) De Rijksuniversiteit Groningen Groningen The Netherlands
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology University of Gothenburg Gothenburg Sweden
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14
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He Y, Cooney CR, Maddock S, Thomas GH. Using pose estimation to identify regions and points on natural history specimens. PLoS Comput Biol 2023; 19:e1010933. [PMID: 36812227 PMCID: PMC9987800 DOI: 10.1371/journal.pcbi.1010933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/06/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
A key challenge in mobilising growing numbers of digitised biological specimens for scientific research is finding high-throughput methods to extract phenotypic measurements on these datasets. In this paper, we test a pose estimation approach based on Deep Learning capable of accurately placing point labels to identify key locations on specimen images. We then apply the approach to two distinct challenges that each requires identification of key features in a 2D image: (i) identifying body region-specific plumage colouration on avian specimens and (ii) measuring morphometric shape variation in Littorina snail shells. For the avian dataset, 95% of images are correctly labelled and colour measurements derived from these predicted points are highly correlated with human-based measurements. For the Littorina dataset, more than 95% of landmarks were accurately placed relative to expert-labelled landmarks and predicted landmarks reliably captured shape variation between two distinct shell ecotypes ('crab' vs 'wave'). Overall, our study shows that pose estimation based on Deep Learning can generate high-quality and high-throughput point-based measurements for digitised image-based biodiversity datasets and could mark a step change in the mobilisation of such data. We also provide general guidelines for using pose estimation methods on large-scale biological datasets.
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Affiliation(s)
- Yichen He
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield; Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| | - Christopher R. Cooney
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield; Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
| | - Steve Maddock
- Department of Computer Science, University of Sheffield; Regent Court, University of Sheffield, Sheffield, United Kingdom
| | - Gavin H. Thomas
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield; Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
- Bird Group, Department of Life Sciences, The Natural History Museum at Tring; Tring, United Kingdom
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15
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Westram AM, Butlin R. Professor Kerstin Johannesson-winner of the 2022 Molecular Ecology Prize. Mol Ecol 2023; 32:26-29. [PMID: 36443277 DOI: 10.1111/mec.16779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Anja Marie Westram
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Roger Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, Strömstad, Sweden
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16
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Ahrens CW, Watson‐Lazowski A, Huang G, Tissue DT, Rymer PD. The roles of divergent and parallel molecular evolution contributing to thermal adaptive strategies in trees. PLANT, CELL & ENVIRONMENT 2022; 45:3476-3491. [PMID: 36151708 PMCID: PMC9828096 DOI: 10.1111/pce.14449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Local adaptation is a driver of biological diversity, and species may develop analogous (parallel evolution) or alternative (divergent evolution) solutions to similar ecological challenges. We expect these adaptive solutions would culminate in both phenotypic and genotypic signals. Using two Eucalyptus species (Eucalyptus grandis and Eucalyptus tereticornis) with overlapping distributions grown under contrasting 'local' temperature conditions to investigate the independent contribution of adaptation and plasticity at molecular, physiological and morphological levels. The link between gene expression and traits markedly differed between species. Divergent evolution was the dominant pattern driving adaptation (91% of all significant genes); but overlapping gene (homologous) responses were dependent on the determining factor (plastic, adaptive or genotype by environment interaction). Ninety-eight percent of the plastic homologs were similarly regulated, while 50% of the adaptive homologs and 100% of the interaction homologs were antagonistical. Parallel evolution for the adaptive effect in homologous genes was greater than expected but not in favour of divergent evolution. Heat shock proteins for E. grandis were almost entirely driven by adaptation, and plasticity in E. tereticornis. These results suggest divergent molecular evolutionary solutions dominated the adaptive mechanisms among species, even in similar ecological circumstances. Suggesting that tree species with overlapping distributions are unlikely to equally persist in the future.
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Affiliation(s)
- Collin W. Ahrens
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Research Centre for Ecosystem ResilienceRoyal Botanic Gardens and Domain TrustSydneyNew South WalesAustralia
| | - Alexander Watson‐Lazowski
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- John Innes CentreNorwich Research ParkNorwichUK
| | - Guomin Huang
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
| | - David T. Tissue
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
- Global Centre for Land‐Based Innovation, Hawkesbury CampusWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Paul D. Rymer
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
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17
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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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18
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Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Evolution 2022; 76:2332-2346. [PMID: 35994296 PMCID: PMC9826283 DOI: 10.1111/evo.14602] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/24/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.
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Affiliation(s)
- Eva L. Koch
- School of BiosciencesUniversity of SheffieldSheffieldUK,Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Mark Ravinet
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Anja M. Westram
- Institute of Science and Technology Austria (ISTA)KlosterneuburgAustria,Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Kerstin Johannesson
- Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
| | - Roger K. Butlin
- School of BiosciencesUniversity of SheffieldSheffieldUK,Marine Science, Tjärnö Marine LaboratoryUniversity of GothenburgGothenburgSweden
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19
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Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. Differing associations between sex determination and sex‐linked inversions in two ecotypes of
Littorina saxatilis. Evol Lett 2022; 6:358-374. [PMID: 36254259 PMCID: PMC9554762 DOI: 10.1002/evl3.295] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022] Open
Abstract
Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex‐determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex‐determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex‐determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment‐dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well‐studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female‐heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion‐sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex‐determining region between ecotypes. Such sex chromosome‐environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex‐specific selection and divergent natural selection is required to explain these highly unusual patterns.
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Affiliation(s)
- Katherine E. Hearn
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
| | - Eva L. Koch
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Sean Stankowski
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- ISTA (Institute of Science and Technology Austria) Klosterneuburg 3400 Austria
| | - Roger K. Butlin
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- Department of Marine Sciences University of Gothenburg Strömstad SE‐45296 Sweden
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Campus de Vairão, Universidade do Porto Vairão 4485‐661 Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO Campus de Vairão, Universidade do Porto Vairão 4485‐661 Portugal
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad SE‐45296 Sweden
| | - Anja M. Westram
- ISTA (Institute of Science and Technology Austria) Klosterneuburg 3400 Austria
- Faculty of Biosciences and Aquaculture Nord University Bodø 8026 Norway
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20
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Westram AM, Faria R, Johannesson K, Butlin R, Barton N. Inversions and parallel evolution. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210203. [PMID: 35694747 PMCID: PMC9189493 DOI: 10.1098/rstb.2021.0203] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Anja M Westram
- ISTA (Institute of Science and Technology Austria), Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.,Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Roger Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nick Barton
- ISTA (Institute of Science and Technology Austria), Klosterneuburg, Austria
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21
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Clark JD, Benham PM, Maldonado JE, Luther DA, Lim HC. Maintenance of local adaptation despite gene flow in a coastal songbird. Evolution 2022; 76:1481-1494. [PMID: 35700208 PMCID: PMC9545442 DOI: 10.1111/evo.14538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 01/22/2023]
Abstract
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
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Affiliation(s)
- Jonathan D. Clark
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Current Address: Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire03824
| | - Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Jesus E. Maldonado
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013
| | - David A. Luther
- Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
| | - Haw Chuan Lim
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013,Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
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22
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De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraïsse C. Ten years of demographic modelling of divergence and speciation in the sea. Evol Appl 2022; 16:542-559. [PMID: 36793688 PMCID: PMC9923478 DOI: 10.1111/eva.13428] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the 'grey zone of speciation' for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.
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Affiliation(s)
- Aurélien De Jode
- Department of Marine Sciences‐TjärnöUniversity of GothenburgGothenburgSweden
| | - Alan Le Moan
- Department of Marine Sciences‐TjärnöUniversity of GothenburgGothenburgSweden
| | - Kerstin Johannesson
- Department of Marine Sciences‐TjärnöUniversity of GothenburgGothenburgSweden
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal,BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Sean Stankowski
- Institute of Science and Technology Austria (IST Austria)KlosterneuburgAustria
| | - Anja Marie Westram
- Institute of Science and Technology Austria (IST Austria)KlosterneuburgAustria,Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Roger K. Butlin
- Department of Marine Sciences‐TjärnöUniversity of GothenburgGothenburgSweden,Ecology and Evolutionary Biology, School of BiosciencesThe University of SheffieldSheffieldUK
| | - Marina Rafajlović
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
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23
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The rise and fall of an alien: why the successful colonizer Littorina saxatilis failed to invade the Mediterranean Sea. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02838-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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24
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Fernández-Meirama M, Rolán-Alvarez E, Carvajal-Rodríguez A. A Simulation Study of the Ecological Speciation Conditions in the Galician Marine Snail Littorina saxatilis. Front Genet 2022; 13:680792. [PMID: 35480312 PMCID: PMC9037070 DOI: 10.3389/fgene.2022.680792] [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: 03/15/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
In the last years, the interest in evolutionary divergence at small spatial scales has increased and so did the study of speciation caused by ecologically based divergent natural selection. The evolutionary interplay between gene flow and local adaptation can lead to low-dispersal locally adapted specialists. When this occurs, the evolutionary interplay between gene flow and local adaptation could eventually lead to speciation. The L. saxatilis system consists of two ecotypes displaying a microhabitat-associated intraspecific dimorphism along the wave-exposed rocky shores of Galicia. Despite being a well-known system, the dynamics of the ecotype formation remain unclear and cannot be studied from empirical evidence alone. In this study, individual-based simulations were used to incorporate relevant ecological, spatial, and genetic information, to check different evolutionary scenarios that could evolve non-random mating preferences and finally may facilitate speciation. As main results, we observed the evolution of intermediate values of choice which matches the estimates from empirical data of L. saxatilis in Galician shores and coincides with previous theoretical outcomes. Also, the use of the mating correlation as a proxy for assortative mating led to spuriously inferring greater reproductive isolation in the middle habitat than in the others, which does not happen when directly considering the choice values from the simulations. We also corroborate the well-known fact that the occurrence of speciation is influenced by the strength of selection. Taken together, this means, also according to other L. saxatilis systems, that speciation is not an immediate consequence of local divergent selection and mating preferences, but a fine tuning among several factors including the ecological conditions in the shore levels, the selection strength, the mate choice stringency, and cost to choosiness. The L. saxatilis system could correspond to a case of incomplete reproductive isolation, where the choice intensity is intermediate and local adaptation within the habitat is strong. These results support previous interpretations of the L. saxatilis model system and indicate that further empirical studies would be interesting to test whether the mate choice mechanism functions as a similarity-like mechanism as has been shown in other littorinids.
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Affiliation(s)
- M Fernández-Meirama
- Departamento de Bioquímica, Genética e Inmunología and Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
| | - E Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología and Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
| | - A Carvajal-Rodríguez
- Departamento de Bioquímica, Genética e Inmunología and Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
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25
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Fark SN, Gerber S, Alonzo SH, Kindsvater HK, Meier JI, Seehausen O. Multispecies colour polymorphisms associated with contrasting microhabitats in two Mediterranean wrasse radiations. J Evol Biol 2022; 35:633-647. [PMID: 35304789 PMCID: PMC9311657 DOI: 10.1111/jeb.13999] [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: 12/08/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 12/01/2022]
Abstract
Intraspecific colour polymorphisms (CPs) present unique opportunities to study fundamental evolutionary questions, such as the link between ecology and phenotype, mechanisms maintaining genetic diversity and their putative role in speciation. Wrasses are highly diverse in ecology and morphology and harbour a variety of colour‐polymorphic species. In the Mediterranean Sea, wrasses of the tribe Labrini evolved two species radiations each harbouring several species with a brown and a green morph. The colour morphs occur in complete sympatry in mosaic habitats with rocky outcrops and Neptune grass patches. Morph‐specific differences had not been characterized yet and the evolutionary forces maintaining them remained unknown. With genome‐wide data for almost all Labrini species, we show that species with CPs are distributed across the phylogeny, but show evidence of hybridization. This suggests that the colour morphs are either ancient and have been lost repeatedly, that they have evolved repeatedly or have been shared via hybridization. Focusing on two polymorphic species, we find that each colour morph is more common in the microhabitat providing the best colour match and that the morphs exhibit additional behavioural and morphological differences further improving crypsis in their respective microhabitats. We find little evidence for genetic differentiation between the morphs in either species. Therefore, we propose that these colour morphs represent a multi‐niche polymorphism as an adaptation to the highly heterogeneous habitat. Our study highlights how colour polymorphism (CP) can be advantageous in mosaic habitats and that Mediterranean wrasses are an ideal system to study trans‐species polymorphisms, i.e. polymorphisms maintained across several species, in adaptive radiations.
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Affiliation(s)
- Sarya N Fark
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Steve Gerber
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Suzanne H Alonzo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
| | - Holly K Kindsvater
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Zoology, University of Cambridge, Cambridge, UK.,Center of Ecology, Evolution & Biogeochemistry, Swiss Institute for Environmental Sciences and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Center of Ecology, Evolution & Biogeochemistry, Swiss Institute for Environmental Sciences and Technology (EAWAG), Kastanienbaum, Switzerland
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26
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Durán-Castillo M, Hudson A, Wilson Y, Field DL, Twyford AD. A phylogeny of Antirrhinum reveals parallel evolution of alpine morphology. THE NEW PHYTOLOGIST 2022; 233:1426-1439. [PMID: 34170548 DOI: 10.1111/nph.17581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Parallel evolution of similar morphologies in closely related lineages provides insight into the repeatability and predictability of evolution. In the genus Antirrhinum (snapdragons), as in other plants, a suite of morphological characters are associated with adaptation to alpine environments. We tested for parallel trait evolution in Antirrhinum by investigating phylogenetic relationships using restriction-site associated DNA (RAD) sequencing. We then associated phenotypic information to our phylogeny to reconstruct the patterns of morphological evolution and related this to evidence for hybridisation between emergent lineages. Phylogenetic analyses showed that the alpine character syndrome is present in multiple groups, suggesting that Antirrhinum has repeatedly colonised alpine habitats. Dispersal to novel environments happened in the presence of intraspecific and interspecific gene flow. We found support for a model of parallel evolution in Antirrhinum. Hybridisation in natural populations, and a complex genetic architecture underlying the alpine morphology syndrome, support an important role of natural selection in maintaining species divergence in the face of gene flow.
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Affiliation(s)
- Mario Durán-Castillo
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yvette Wilson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David L Field
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, 6027, Australia
| | - Alex D Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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27
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Felmy A, Reznick DN, Travis J, Potter T, Coulson T. Life histories as mosaics: plastic and genetic components differ among traits that underpin life-history strategies. Evolution 2022; 76:585-604. [PMID: 35084046 PMCID: PMC9303950 DOI: 10.1111/evo.14440] [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: 02/11/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Life‐history phenotypes emerge from clusters of traits that are the product of genes and phenotypic plasticity. If the impact of the environment differs substantially between traits, then life histories might not evolve as a cohesive whole. We quantified the sensitivity of components of the life history to food availability, a key environmental difference in the habitat occupied by contrasting ecotypes, for 36 traits in fast‐ and slow‐reproducing Trinidadian guppies. Our dataset included six putatively independent origins of the slow‐reproducing, derived ecotype. Traits varied substantially in plastic and genetic control. Twelve traits were influenced only by food availability (body lengths, body weights), five only by genetic differentiation (interbirth intervals, offspring sizes), 10 by both (litter sizes, reproductive timing), and nine by neither (fat contents, reproductive allotment). Ecotype‐by‐food interactions were negligible. The response to low food was aligned with the genetic difference between high‐ and low‐food environments, suggesting that plasticity was adaptive. The heterogeneity among traits in environmental sensitivity and genetic differentiation reveals that the components of the life history may not evolve in concert. Ecotypes may instead represent mosaics of trait groups that differ in their rate of evolution.
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Affiliation(s)
- Anja Felmy
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, United Kingdom
| | - David N Reznick
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California, 922521, USA
| | - Joseph Travis
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306, USA
| | - Tomos Potter
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, United Kingdom
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, United Kingdom
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28
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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29
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de Aranzamendi MC, Martínez JJ, Held C, Sahade R. Parallel shape divergence between ecotypes of the limpet Nacella concinna along the Antarctic Peninsula: a new model species for parallel evolution? ZOOLOGY 2021; 150:125983. [PMID: 34915245 DOI: 10.1016/j.zool.2021.125983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/23/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
Parallel phenotypic divergence is the independent differentiation between phenotypes of the same lineage or species occupying ecologically similar environments in different populations. We tested in the Antarctic limpet Nacella concinna the extent of parallel morphological divergence in littoral and sublittoral ecotypes throughout its distribution range. These ecotypes differ in morphological, behavioural and physiological characteristics. We studied the lateral and dorsal outlines of shells and the genetic variation of the mitochondrial gene Cytochrome Oxidase subunit I from both ecotypes in 17 sample sites along more than 2,000 km. The genetic data indicate that both ecotypes belong to a single evolutionary lineage. The magnitude and direction of phenotypic variation differ between ecotypes across sample sites; completely parallel ecotype-pairs (i.e., they diverge in the same magnitude and in the same direction) were detected in 84.85% of lateral and 65.15% in dorsal view comparisons. Besides, specific traits (relative shell height, position of shell apex, and elliptical/pear-shape outline variation) showed high parallelism. We observed weak morphological covariation between the two shape shell views, indicating that distinct evolutionary forces and environmental pressures could be acting on this limpet shell shape. Our results demonstrate there is a strong parallel morphological divergence pattern in N. concinna along its distribution, making this Antarctic species a suitable model for the study of different evolutionary forces shaping the shell evolution of this limpet.
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Affiliation(s)
- María Carla de Aranzamendi
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Ecología Marina, Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Ecosistemas Marinos y Polares (ECOMARES), Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina.
| | - Juan José Martínez
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), CONICET and Universidad Nacional de Jujuy, C. Gorriti 237, San Salvador de Jujuy, 4600, Argentina.
| | - Christoph Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany.
| | - Ricardo Sahade
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Ecología Marina, Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Ecosistemas Marinos y Polares (ECOMARES), Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina.
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30
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James ME, Arenas-Castro H, Groh JS, Allen SL, Engelstädter J, Ortiz-Barrientos D. Highly Replicated Evolution of Parapatric Ecotypes. Mol Biol Evol 2021; 38:4805-4821. [PMID: 34254128 PMCID: PMC8557401 DOI: 10.1093/molbev/msab207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origins of ecotypes are often inferred based on a phylogeny that clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic because gene flow and incomplete lineage sorting can uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography and show that this is unlikely due to gene flow between parapatric ecotypes, which was surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Henry Arenas-Castro
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Scott L Allen
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
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31
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James ME, Wilkinson MJ, Bernal DM, Liu H, North HL, Engelstädter J, Ortiz-Barrientos D. Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio. Evolution 2021; 75:3115-3131. [PMID: 34687472 PMCID: PMC9299460 DOI: 10.1111/evo.14387] [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] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune‐Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait‐environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Diana M Bernal
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Biousos Neotropicales S.A.S, Bogotá, Colombia
| | - Huanle Liu
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Henry L North
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
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32
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Zerebecki RA, Sotka EE, Hanley TC, Bell KL, Gehring C, Nice CC, Richards CL, Hughes AR. Repeated Genetic and Adaptive Phenotypic Divergence across Tidal Elevation in a Foundation Plant Species. Am Nat 2021; 198:E152-E169. [DOI: 10.1086/716512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Robyn A. Zerebecki
- Marine Science Center, Northeastern University, Nahant, Massachusetts 01908
- Dauphin Island Sea Lab, Dauphin Island, Alabama 36528
| | - Erik E. Sotka
- Department of Biology and Grice Marine Laboratory, College of Charleston, South Carolina 29412
| | - Torrance C. Hanley
- Marine Science Center, Northeastern University, Nahant, Massachusetts 01908
| | - Katherine L. Bell
- Department of Entomology, University of Maryland, College Park, Maryland 20742
| | - Catherine Gehring
- Department of Biological Science and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, Arizona 86011
| | - Chris C. Nice
- Department of Biology, Texas State University, San Marcos, Texas 78666
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33617; and Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany
| | - A. Randall Hughes
- Marine Science Center, Northeastern University, Nahant, Massachusetts 01908
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33
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Dwane C, Rundle SD, Tills O, Rezende EL, Galindo J, Rolán-Alvarez E, Truebano M. Divergence in Thermal Physiology Could Contribute to Vertical Segregation in Intertidal Ecotypes of Littorina saxatilis. Physiol Biochem Zool 2021; 94:353-365. [PMID: 34431748 DOI: 10.1086/716176] [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] [Indexed: 11/03/2022]
Abstract
AbstractThermal stress is a potentially important selective agent in intertidal marine habitats, but the role that thermal tolerance might play in local adaptation across shore height has been underexplored. Northwest Spain is home to two morphologically distinct ecotypes of the periwinkle Littorina saxatilis, separated by shore height and subject to substantial differences in thermal stress exposure. However, despite other biotic and abiotic drivers of ecotype segregation being well studied, their thermal tolerance has not been previously characterized. We investigated thermal tolerance across multiple life history stages by employing the thermal death time (TDT) approach to determine (i) whether the two ecotypes differ in thermal tolerance and (ii) how any differences vary with life history stage. Adults of the two ecotypes differed in their thermal tolerance in line with their shore position: the upper-shore ecotype, which experiences more extreme temperatures, exhibited greater endurance of thermal stress compared with the lower-shore ecotype. This difference was most pronounced at the highest temperatures tested. The proximate physiological basis for these differences is unknown but likely due to a multifarious interaction of traits affecting different parts of the TDT curve. Differences in tolerance between ecotypes were less pronounced in early life history stages but increased with ontogeny, suggesting partial divergence of this trait during development. Thermal tolerance could potentially play an important role in maintaining population divergence and genetic segregation between the two ecotypes, since the increased thermal sensitivity of the lower-shore ecotype may limit its dispersal onto the upper shore and so restrict gene flow.
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34
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Rainha RN, Martinez PA, Moraes LJCL, Castro KMSA, Réjaud A, Fouquet A, Leite RN, Rodrigues MT, Werneck FP. Subtle environmental variation affects phenotypic differentiation of shallow divergent treefrog lineages in Amazonia. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Abstract
Amazonia harbours a vast biotic and ecological diversity, enabling investigation of the effects of microevolutionary processes and environmental variation on species diversification. Integrative approaches combining phenotypic and genetic variation can improve our knowledge on diversification processes in megadiverse regions. Here, we investigate the influence of environmental and geographic variation on the genetic and morphological differentiation in the Amazonian Boana calcarata-fasciata (Anura: Hylidae) species complex. We analysed the variation of one mtDNA gene from individuals of different forest environments, and assessed their phylogenetic relationships and species limits to define the lineages to perform a phenotypic-environmental approach. We collected morphological data (head shape and size) using 3D models and investigated the phylogenetic signal, evolutionary model and influence of environmental variables on morphology. We verified associations between environmental and geographical distances with morphological and genetic variation using distance-based redundancy analyses and Mantel tests. We found an even higher cryptic diversity than already recognized within the species complex. Body size and head shape varied among specimens, but did not present phylogenetic signal, diverging under a selective evolutionary model. Our results show that diverse factors have influenced morphological and genetic variation, but environmental conditions such as vegetation cover, precipitation and climate change velocity influenced morphological diversification. Possible population-level mechanisms such as parallel morphological evolution or plastic responses to similar environments could account for such patterns in these typical Amazonian treefrogs.
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Affiliation(s)
- Raíssa N Rainha
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
| | - Pablo A Martinez
- Laboratorio de Pesquisas Integrativas em Biodiversidade, Departamento de Biologia, Universidade Federal de Sergipe, Avenida Marechal Rondon, Aracaju, Sergipe, Brazil
| | - Leandro J C L Moraes
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
| | - Kathleen M S A Castro
- Laboratorio de Pesquisas Integrativas em Biodiversidade, Departamento de Biologia, Universidade Federal de Sergipe, Avenida Marechal Rondon, Aracaju, Sergipe, Brazil
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier, Bâtiment, CNRS, IRD, Toulouse, France
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier, Bâtiment, CNRS, IRD, Toulouse, France
| | - Rafael N Leite
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Universidade de São Paulo Instituto de Biociências, Rua do Matão, travessa, nº. São Paulo, São Paulo, Brazil
| | - Fernanda P Werneck
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
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35
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Maltseva AL, Varfolomeeva MA, Ayanka RV, Gafarova ER, Repkin EA, Pavlova PA, Shavarda AL, Mikhailova NA, Granovitch AI. Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus Littorina ( Neritrema). Ecol Evol 2021; 11:11134-11154. [PMID: 34429908 PMCID: PMC8366845 DOI: 10.1002/ece3.7901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/08/2021] [Accepted: 06/22/2021] [Indexed: 12/03/2022] Open
Abstract
Divergence of ecological niches in phylogenetically closely related species indicates the importance of ecology in speciation, especially for sympatric species are considered. Such ecological diversification provides an advantage of alleviating interspecies competition and promotes more efficient exploitation of environmental resources, thus being a basis for ecological speciation. We analyzed a group of closely related species from the subgenus Neritrema (genus Littorina, Caenogastropoda) from the gravel-bouldery shores. In two distant sites at the Barents and Norwegian Sea, we examined the patterns of snail distribution during low tide (quantitative sampling stratified by intertidal level, presence of macrophytes, macrophyte species, and position on them), shell shape and its variability (geometric morphometrics), and metabolic characteristics (metabolomic profiling). The studied species diversified microbiotopes, which imply an important role of ecological specification in the recent evolution of this group. The only exception to this trend was the species pair L. arcana / L. saxatilis, which is specifically discussed. The ecological divergence was accompanied by differences in shell shape and metabolomic characteristics. Significant differences were found between L. obtusata versus L. fabalis and L. saxatilis / L. arcana versus L. compressa both in shell morphology and in metabolomes. L. saxatilis demonstrated a clear variability depending on intertidal level which corresponds to a shift in conditions within the occupied microhabitat. Interestingly, the differences between L. arcana (inhabiting the upper intertidal level) and L. compressa (inhabiting the lower one) were analogous to those between the upper and lower fractions of L. saxatilis. No significant level-dependent changes were found between the upper and lower fractions of L. obtusata, most probably due to habitat amelioration by fucoid macroalgae. All these results are discussed in the contexts of the role of ecology in speciation, ecological niche dynamics and conservatism, and evolutionary history of the Neritrema species.
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Affiliation(s)
- Arina L Maltseva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Roman V Ayanka
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Elizaveta R Gafarova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Egor A Repkin
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Polina A Pavlova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Alexei L Shavarda
- Department of Analytical Phytochemistry Komarov Botanical Institute St. Petersburg Russia
- Research Park Centre for Molecular and Cell Technologies St. Petersburg State University St. Petersburg Russia
| | - Natalia A Mikhailova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
- Centre of Cell Technologies Institute of Cytology Russian Academy of Sciences St. Petersburg Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
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36
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Diz AP, Romero MR, Galindo J, Saura M, Skibinski DOF, Rolán-Alvarez E. Proteomic analysis of F1 hybrids and intermediate variants in a littorina saxatilis hybrid zone. Curr Zool 2021; 68:351-359. [PMID: 35592345 PMCID: PMC9113252 DOI: 10.1093/cz/zoab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022] Open
Abstract
Proteomic analysis was carried out on the Crab (upper-shore) and Wave (lower-shore) ecotypes of Littorina saxatilis from a hybrid zone at Silleiro Cape, Spain. Proteome profiles of individual snails were obtained. Protein expression in F1 hybrid snails bred in the laboratory and snails with intermediate shell phenotypes collected from the mid-shore were compared with Crab and Wave ecotypes using analytical approaches used to study dominance. Multivariate analysis over many protein spots showed that the F1 snails are distinct from both ecotypes but closer to the Wave ecotype. The intermediate snails are highly variable, some closer to the Crab and others to the Wave ecotype. Considered on a protein by protein basis, some proteins are significantly closer in expression to the Crab and others to the Wave ecotype for both F1 and intermediate snails. Furthermore, a significant majority of proteins were closer in expression to the Wave ecotype for the F1, consistent with the multivariate analysis. No such significant majority toward either the Crab or Wave ecotype was observed for the intermediate snails. The closer similarity of F1 and Wave ecotype expression patterns could be the result of similar selective pressures in the similar mid-shore and low-shore environments. For a significantly larger number of proteins, intermediate snails were closer in expression to the ecotype having the lower expression, for both Crab and Wave ecotypes. This is somewhat unexpected as lower expression might be expected to be an indication of impairment of function and lower fitness. Proteomic analysis could be important for the identification of candidate proteins useful for gaining improved understanding of adaptation and barriers to gene flow in hybrid zones.
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Affiliation(s)
- Angel P Diz
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
- Address Correspondence to Angel P. Diz. E-mail:
| | - Mónica R Romero
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
| | - Juan Galindo
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Madrid 28040, Spain
| | - David O F Skibinski
- Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK
| | - Emilio Rolán-Alvarez
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
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37
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Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Mol Ecol 2021; 30:3797-3814. [PMID: 33638231 DOI: 10.1111/mec.15861] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/12/2021] [Indexed: 12/28/2022]
Abstract
Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder-rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.
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Affiliation(s)
- Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Kerstin Johannesson
- Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger Butlin
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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38
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Yong L, Croft DP, Troscianko J, Ramnarine IW, Wilson AJ. Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space. Mol Ecol 2021; 31:1337-1357. [PMID: 34170592 DOI: 10.1111/mec.16039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/29/2021] [Accepted: 06/16/2021] [Indexed: 12/01/2022]
Abstract
Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy (Poecilia reticulata). In guppies, colonisation of low predation habitats is associated with emergence of 'more colourful' phenotypes since predator-induced viability selection for crypsis weakens while sexual selection by female preference for conspicuousness remains strong. Our study differs from previous investigations in three respects. First, we adopted a multivariate phenotyping approach to characterise parallelism in multitrait space. Second, we used ecologically-relevant colour traits defined by the visual systems of the two selective agents (i.e., guppy, predatory cichlid). Third, we estimated population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypic divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model but very limited support for the predicted pattern of greater conspicuousness at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely nonsignificant, and explained little among-population variation. In multitrait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation, potentially by female choice, but suggest that this proceeds in independent directions of multitrait space across lineages. Pool-sequencing data also revealed SNPs showing greater differentiation than expected under neutrality, among which some are found in genes contributing to colour pattern variation, presenting opportunities for future genetic study.
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Affiliation(s)
- Lengxob Yong
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Darren P Croft
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Jolyon Troscianko
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Indar W Ramnarine
- Department of Life Sciences, The University of The West Indies, St Augustine, Trinidad and Tobago
| | - Alastair J Wilson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
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39
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Brachmann MK, Parsons K, Skúlason S, Ferguson MM. The interaction of resource use and gene flow on the phenotypic divergence of benthic and pelagic morphs of Icelandic Arctic charr ( Salvelinus alpinus). Ecol Evol 2021; 11:7315-7334. [PMID: 34188815 PMCID: PMC8216915 DOI: 10.1002/ece3.7563] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Conceptual models of adaptive divergence and ecological speciation in sympatry predict differential resource use, phenotype-environment correlations, and reduced gene flow among diverging phenotypes. While these predictions have been assessed in past studies, connections among them have rarely been assessed collectively. We examined relationships among phenotypic, ecological, and genetic variation in Arctic charr (Salvelinus alpinus) from six Icelandic localities that have undergone varying degrees of divergence into sympatric benthic and pelagic morphs. We characterized morphological variation with geometric morphometrics, tested for differential resource use between morphs using stable isotopes, and inferred the amount of gene flow from single nucleotide polymorphisms. Analysis of stable isotopic signatures indicated that sympatric morphs showed similar difference in resource use across populations, likely arising from the common utilization of niche space within each population. Carbon isotopic signature was also a significant predictor of individual variation in body shape and size, suggesting that variation in benthic and pelagic resource use is associated with phenotypic variation. The estimated percentage of hybrids between sympatric morphs varied across populations (from 0% to 15.6%) but the majority of fish had genotypes (ancestry coefficients) characteristic of pure morphs. Despite evidence of reduced gene flow between sympatric morphs, we did not detect the expected negative relationship between divergence in resource use and gene flow. Three lakes showed the expected pattern, but morphs in the fourth showed no detectable hybridization and had relatively low differences in resource use between them. This coupled with the finding that resource use and genetic differentiation had differential effects on body shape variation across populations suggests that reproductive isolation maintains phenotypic divergence between benthic and pelagic morphs when the effects of resource use are relatively low. Our ability to assess relationships between phenotype, ecology, and genetics deepens our understanding of the processes underlying adaptive divergence in sympatry.
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Affiliation(s)
| | - Kevin Parsons
- Institute of Biodiversity, Animal Health and Comparative MedicineSchool of Life ScienceUniversity of GlasgowGlasgowUK
| | - Skúli Skúlason
- Department of Aquaculture and Fish BiologyHólar UniversitySaudárkrókurIceland
- Icelandic Museum of Natural HistoryReykjavíkIceland
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40
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Hancock ZB, Lehmberg ES, Bradburd GS. Neo-darwinism still haunts evolutionary theory: A modern perspective on Charlesworth, Lande, and Slatkin (1982). Evolution 2021; 75:1244-1255. [PMID: 33999415 PMCID: PMC8979413 DOI: 10.1111/evo.14268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 12/31/2022]
Abstract
The Modern Synthesis (or "Neo-Darwinism"), which arose out of the reconciliation of Darwin's theory of natural selection and Mendel's research on genetics, remains the foundation of evolutionary theory. However, since its inception, it has been a lightning rod for criticism, which has ranged from minor quibbles to complete dismissal. Among the most famous of the critics was Stephen Jay Gould, who, in 1980, proclaimed that the Modern Synthesis was "effectively dead." Gould and others claimed that the action of natural selection on random mutations was insufficient on its own to explain patterns of macroevolutionary diversity and divergence, and that new processes were required to explain findings from the fossil record. In 1982, Charlesworth, Lande, and Slatkin published a response to this critique in Evolution, in which they argued that Neo-Darwinism was indeed sufficient to explain macroevolutionary patterns. In this Perspective for the 75th Anniversary of the Society for the Study of Evolution, we review Charlesworth et al. in its historical context and provide modern support for their arguments. We emphasize the importance of microevolutionary processes in the study of macroevolutionary patterns. Ultimately, we conclude that punctuated equilibrium did not represent a major revolution in evolutionary biology - although debate on this point stimulated significant research and furthered the field - and that Neo-Darwinism is alive and well.
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Affiliation(s)
- Zachary B. Hancock
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan
| | - Emma S. Lehmberg
- Department of Biology, Texas A&M University, College Station, Texas
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, College Station, Texas
| | - Gideon S. Bradburd
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan
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41
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Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evol Lett 2021; 5:196-213. [PMID: 34136269 PMCID: PMC8190449 DOI: 10.1002/evl3.227] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 01/11/2023] Open
Abstract
Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
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Affiliation(s)
- Eva L Koch
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Hernán E Morales
- Evolutionary Genetics Section Globe Institute University of Copenhagen Copenhagen Denmark.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Jenny Larsson
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Anja M Westram
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,IST Austria Klosterneuburg Austria
| | - Rui Faria
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida FL 32306-4120
| | - E Moriarty Lemmon
- Department of Biological Science Florida State University Tallahassee Florida FL 32306-4295
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
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42
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Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino. Heredity (Edinb) 2021; 126:831-845. [PMID: 33510467 PMCID: PMC8102582 DOI: 10.1038/s41437-021-00408-x] [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: 07/17/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.
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43
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Flanagan SP, Rose E, Jones AG. The population genomics of repeated freshwater colonizations by Gulf pipefish. Mol Ecol 2021; 30:1672-1687. [PMID: 33580570 DOI: 10.1111/mec.15841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/30/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022]
Abstract
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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44
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Kaiser TS, von Haeseler A, Tessmar-Raible K, Heckel DG. Timing strains of the marine insect Clunio marinus diverged and persist with gene flow. Mol Ecol 2021; 30:1264-1280. [PMID: 33410230 DOI: 10.1111/mec.15791] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Genetic divergence of populations in the presence of gene flow is a central theme in speciation research. Theory predicts that divergence can happen with full range overlap - in sympatry - driven by ecological factors, but there are few empirical examples of how ecologically divergent selection can overcome gene flow and lead to reproductive isolation. In the marine midge Clunio marinus (Diptera: Chironomidae) reproduction is ecologically restricted to the time of the lowest tides, which is ensured through accurate control of development and adult emergence by circalunar and circadian clocks. As tidal regimes differ along the coastline, locally adapted timing strains of C. marinus are found in different sites across Europe. At the same time, ecologically suitable low tides occur at both full and new moon and twice a day, providing C. marinus with four nonoverlapping temporal niches at every geographic location. Along the coast of Brittany, which is characterized by a steep gradient in timing of the tides, we found an unusually large number of differentially adapted timing strains, and the first known instances of sympatric C. marinus strains occupying divergent temporal niches. Analysis of mitochondrial genotypes suggests that these timing strains originated from a single recent colonization event. Nuclear genotypes show strong gene flow, sympatric timing strains being the least differentiated. Even when sympatric strains exist in nonoverlapping temporal niches, timing adaptations do not result in genome-wide genetic divergence, suggesting timing adaptations are maintained by permanent ecological selection. This constitutes a model case for incipient ecological divergence with gene flow.
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Affiliation(s)
- Tobias S Kaiser
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.,Max Perutz Laboratories, University of Vienna, Vienna, Austria.,Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | | | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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45
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Choo LQ, Bal TMP, Goetze E, Peijnenburg KTCA. Oceanic dispersal barriers in a holoplanktonic gastropod. J Evol Biol 2021; 34:224-240. [PMID: 33150701 PMCID: PMC7894488 DOI: 10.1111/jeb.13735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/02/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large-scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N-36°S) for the pteropod Limacina bulimoides. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI ΦST = 0.230, 28S ΦST = 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15-18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise ΦST comparisons was identified in the equatorial upwelling region (between 15°N and 4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin-scale transect that was sampled 2 years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome-wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.
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Affiliation(s)
- Le Qin Choo
- Plankton Diversity and EvolutionNaturalis Biodiversity CenterLeidenThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Thijs M. P. Bal
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Erica Goetze
- Department of OceanographyUniversity of Hawaiʻi at MānoaHonoluluUSA
| | - Katja T. C. A. Peijnenburg
- Plankton Diversity and EvolutionNaturalis Biodiversity CenterLeidenThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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46
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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47
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Knotek A, Konečná V, Wos G, Požárová D, Šrámková G, Bohutínská M, Zeisek V, Marhold K, Kolář F. Parallel Alpine Differentiation in Arabidopsis arenosa. FRONTIERS IN PLANT SCIENCE 2020; 11:561526. [PMID: 33363550 PMCID: PMC7753741 DOI: 10.3389/fpls.2020.561526] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/16/2020] [Indexed: 05/14/2023]
Abstract
Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.
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Affiliation(s)
- Adam Knotek
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Veronika Konečná
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Guillaume Wos
- Department of Botany, Charles University, Prague, Czechia
| | | | | | - Magdalena Bohutínská
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Vojtěch Zeisek
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Karol Marhold
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Filip Kolář
- Department of Botany, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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48
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Kess T, Brachmann M, Boulding EG. Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly dispersing snail. J Evol Biol 2020; 34:193-207. [PMID: 33108001 DOI: 10.1111/jeb.13724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 09/29/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022]
Abstract
Littorina saxatilis is becoming a model system for understanding the genomic basis of ecological speciation. The parallel formation of crab-adapted ecotypes that exhibit partial reproductive isolation from wave-adapted ecotypes has enabled genomic investigation of conspicuous shell traits. Recent genomic studies suggest that chromosomal rearrangements may enable ecotype divergence by reducing gene flow. However, the genomic architecture of traits that are divergent between ecotypes remains poorly understood. Here, we use 11,504 single nucleotide polymorphism (SNP) markers called using the recently released L. saxatilis genome to genotype 462 crab ecotype, wave ecotype and phenotypically intermediate Spanish L. saxatilis individuals with scored phenotypes. We used redundancy analysis to study the genetic architecture of loci associated with shell shape, shape corrected for size, shell size and shell ornamentation, and to compare levels of co-association among different traits. We discovered 341 SNPs associated with shell traits. Loci associated with trait divergence between ecotypes were often located inside putative chromosomal rearrangements recently characterized in Swedish L. saxatilis. In contrast, we found that shell shape corrected for size varied primarily by geographic site rather than by ecotype and showed little association with these putative rearrangements. We conclude that genomic regions of elevated divergence inside putative rearrangements were associated with divergence of L. saxatilis ecotypes along steep environmental axes-consistent with models of adaptation with gene flow-but were not associated with divergence among the three geographical sites. Our findings support predictions from models indicating the importance of genomic regions of reduced recombination allowing co-association of loci during ecological speciation with ongoing gene flow.
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Affiliation(s)
- Tony Kess
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Matthew Brachmann
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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49
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Galindo J, Carvalho J, Sotelo G, Duvetorp M, Costa D, Kemppainen P, Panova M, Kaliontzopoulou A, Johannesson K, Faria R. Genetic and morphological divergence between Littorina fabalis ecotypes in Northern Europe. J Evol Biol 2020; 34:97-113. [PMID: 32935387 DOI: 10.1111/jeb.13705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/15/2020] [Accepted: 09/07/2020] [Indexed: 01/21/2023]
Abstract
Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared patterns of habitat-related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model-based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.
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Affiliation(s)
- Juan Galindo
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Mariña (CIM-UVIGO), Vigo, Spain
| | - João Carvalho
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| | - Graciela Sotelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Mårten Duvetorp
- Department of Marine Sciences -Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Diana Costa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marina Panova
- Department of Marine Sciences -Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Antigoni Kaliontzopoulou
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Kerstin Johannesson
- Department of Marine Sciences -Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
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50
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Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. The evolution of strong reproductive isolation between sympatric intertidal snails. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190545. [PMID: 32654639 DOI: 10.1098/rstb.2019.0545] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Anja M Westram
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Zuzanna B Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Thomas Broquet
- CNRS and Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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