1
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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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2
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Rosenfeld S, Maturana CS, Spencer HG, Convey P, Saucède T, Brickle P, Bahamonde F, Jossart Q, Poulin E, Gonzalez-Wevar C. Complete distribution of the genus Laevilitorina (Littorinimorpha, Littorinidae) in the Southern Hemisphere: remarks and natural history. Zookeys 2022; 1127:61-77. [PMID: 36760354 PMCID: PMC9836552 DOI: 10.3897/zookeys.1127.91310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/03/2022] [Indexed: 02/11/2023] Open
Abstract
Littorinid snails are present in most coastal areas globally, playing a significant role in the ecology of intertidal communities. Laevilitorina is a marine gastropod genus distributed exclusively in the Southern Hemisphere, with 21 species reported from South America, the sub-Antarctic islands, Antarctica, New Zealand, Australia and Tasmania. Here, an updated database of 21 species generated from a combination of sources is presented: 1) new field sampling data; 2) published records; 3) the Global Biodiversity Information Facility (GBIF) and The Atlas of Living Australia (ALA), to provide a comprehensive description of the known geographic distribution of the genus and detailed occurrences for each of the 21 species. The database includes 813 records (occurrences), 53 from field sampling, 174 from the literature, 128 from GBIF, and 458 from ALA. West Antarctica had the highest species richness (8 species), followed by sub-Antarctic islands of New Zealand (4 species) and the south-east shelf of Australia (4 species). The provinces of Magellan, New Zealand South Island, and sub-Antarctic Islands of the Indian Ocean include two species each. This study specifically highlights reports of L.pygmaea and L.venusta, species that have been almost unrecorded since their description. Recent advances in molecular studies of L.caliginosa showed that this species does not correspond to a widely distributed taxon, but to multiple divergent lineages distributed throughout the Southern Ocean. Ongoing molecular and taxonomic studies are necessary for a better understanding of the diversity and biogeography of this genus.
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Affiliation(s)
- Sebastián Rosenfeld
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile
| | - Claudia S. Maturana
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile,Centro de Investigación Gaia‑Antártica, Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile
| | - Hamish G. Spencer
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Santiago, Chile
| | - Peter Convey
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile,Department of Zoology, University of Otago, Dunedin, New Zealand,British Antarctic Survey (BAS), Cambridge, UK
| | - Thomas Saucède
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Paul Brickle
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6, boulevard Gabriel, 21000, Dijon, France,South Atlantic Environmental Research Institute, Ross Road, Stanley, Falkland Islands, UK
| | - Francisco Bahamonde
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile,Cape Horn International Center (CHIC), Puerto Williams, Chile
| | - Quentin Jossart
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa,School of Biological Sciences (Zoology), University of Aberdeen, Aberdeen, UK
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago, Chile,Centro de Investigación Gaia‑Antártica, Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile
| | - Claudio Gonzalez-Wevar
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago, Chile,Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
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3
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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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4
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Welke CA, Graham B, Conover RR, Rivers JW, Burg TM. Habitat-linked genetic structure for white-crowned sparrow ( Zonotrichia leucophrys): Local factors shape population genetic structure. Ecol Evol 2021; 11:11700-11717. [PMID: 34522334 PMCID: PMC8427623 DOI: 10.1002/ece3.7887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/29/2021] [Accepted: 06/08/2021] [Indexed: 11/15/2022] Open
Abstract
Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modeling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (Zonotrichia leucophrys) subspecies: Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned sparrows do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.
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Affiliation(s)
- Catherine A. Welke
- Department of Biological SciencesUniversity of LethbridgeLethbridgeABCanada
- Department of BiologyThe King's UniversityEdmontonABCanada
| | - Brendan Graham
- Department of Biological SciencesUniversity of LethbridgeLethbridgeABCanada
| | - Ross R. Conover
- Department of Natural SciencesPaul Smith's CollegePaul SmithsNew YorkUSA
| | - James W. Rivers
- Department of Forest Engineering, Resources, and ManagementOregon State UniversityCorvallisOregonUSA
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeABCanada
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5
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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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6
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Magalhaes IS, Whiting JR, D'Agostino D, Hohenlohe PA, Mahmud M, Bell MA, Skúlason S, MacColl ADC. Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations. Nat Ecol Evol 2021; 5:251-261. [PMID: 33257817 PMCID: PMC7858233 DOI: 10.1038/s41559-020-01341-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 10/05/2020] [Indexed: 12/22/2022]
Abstract
Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.
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Affiliation(s)
- Isabel S Magalhaes
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Department of Life Sciences, Whitelands College, University of Roehampton, London, UK.
| | - James R Whiting
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, London, UK.
| | - Daniele D'Agostino
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Muayad Mahmud
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
- Erbil Polytechnic University, Kurdistan Region, Iraq
| | - Michael A Bell
- Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
- Icelandic Museum of Natural History, Suðurlandsbraut, Reykjavík, Iceland
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
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7
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Introduced predator elicits population-specific responses from prey. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02376-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Härer A, Bolnick DI, Rennison DJ. The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback. Mol Ecol 2020; 30:451-463. [PMID: 33222348 DOI: 10.1111/mec.15746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 12/23/2022]
Abstract
The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (FST ) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.
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Affiliation(s)
- Andreas Härer
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Diana J Rennison
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
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9
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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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10
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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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11
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Salisbury SJ, McCracken GR, Perry R, Keefe D, Layton KK, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (
Salvelinus alpinus
). Mol Ecol 2020; 29:4280-4294. [DOI: 10.1111/mec.15634] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Robert Perry
- Department of Environment Fish and Wildlife Division Government of Yukon Whitehorse YT Canada
| | - Donald Keefe
- Department of Environment and Conservation Wildlife Division Government of Newfoundland and Labrador Corner Brook NL Canada
| | - Kara K.S. Layton
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Tony Kess
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
| | - Cameron M. Nugent
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Jong S. Leong
- Department of Biology University of Victoria Victoria BC Canada
| | - Ian R. Bradbury
- Department of Biology Dalhousie University Halifax NS Canada
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria BC Canada
- Centre for Biomedical Research University of Victoria Victoria BC Canada
| | - Moira M. Ferguson
- Department of Integrative Biology University of Guelph Guelph ON Canada
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12
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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: 16] [Impact Index Per Article: 4.0] [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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13
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Zhang M, Suren H, Holliday JA. Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa. Genome Biol Evol 2020; 11:2256-2272. [PMID: 31298685 PMCID: PMC6735766 DOI: 10.1093/gbe/evz151] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/14/2022] Open
Abstract
Local adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype- and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.
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Affiliation(s)
- Man Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia.,National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, China
| | - Haktan Suren
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
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14
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Whiting JR, Fraser BA. Contingent Convergence: The Ability To Detect Convergent Genomic Evolution Is Dependent on Population Size and Migration. G3 (BETHESDA, MD.) 2020; 10:677-693. [PMID: 31871215 PMCID: PMC7003088 DOI: 10.1534/g3.119.400970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/19/2019] [Indexed: 12/02/2022]
Abstract
Outlier scans, in which the genome is scanned for signatures of selection, have become a prominent tool in studies of local adaptation, and more recently studies of genetic convergence in natural populations. However, such methods have the potential to be confounded by features of demographic history, such as population size and migration, which are considerably varied across natural populations. In this study, we use forward-simulations to investigate and illustrate how several measures of genetic differentiation commonly used in outlier scans (FST, DXY and Δπ) are influenced by demographic variation across multiple sampling generations. In a factorial design with 16 treatments, we manipulate the presence/absence of founding bottlenecks (N of founding individuals), prolonged bottlenecks (proportional size of diverging population) and migration rate between two populations with ancestral and diverged phenotypic optima. Our results illustrate known constraints of individual measures associated with reduced population size and a lack of migration; but notably we demonstrate how relationships between measures are similarly dependent on these features of demography. We find that false-positive signals of convergent evolution (the same simulated outliers detected in independent treatments) are attainable as a product of similar population size and migration treatments (particularly for DXY), and that outliers across different measures (for e.g., FST and DXY) can occur with little influence of selection. Taken together, we show how underappreciated, yet quantifiable measures of demographic history can influence commonly employed methods for detecting selection.
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Affiliation(s)
- James R Whiting
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD
| | - Bonnie A Fraser
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD
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15
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Johannesson K, Zagrodzka Z, Faria R, Marie Westram A, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? J Evol Biol 2019; 33:342-351. [PMID: 31724256 PMCID: PMC7079066 DOI: 10.1111/jeb.13570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Zuzanna Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | | | - Roger K Butlin
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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16
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Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. SCIENCE ADVANCES 2019; 5:eaav9963. [PMID: 31840052 PMCID: PMC6892616 DOI: 10.1126/sciadv.aav9963] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.
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Affiliation(s)
- Hernán E. Morales
- Centre for Marine Evolutionary Biology, Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Kerstin Johannesson
- Centre for Marine Evolutionary Biology, Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Tomas Larsson
- Centre for Marine Evolutionary Biology, Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, SE-752 37 Uppsala, Sweden
| | - Marina Panova
- Centre for Marine Evolutionary Biology, Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anja M. Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Centre for Marine Evolutionary Biology, Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
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17
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Porro B, Mallien C, Hume BCC, Pey A, Aubin E, Christen R, Voolstra CR, Furla P, Forcioli D. The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs. Heredity (Edinb) 2019; 124:351-366. [PMID: 31527783 DOI: 10.1038/s41437-019-0266-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 11/09/2022] Open
Abstract
How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
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Affiliation(s)
- Barbara Porro
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
| | - Cédric Mallien
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Benjamin C C Hume
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Alexis Pey
- THALASSA Marine research & Environmental awareness, 17 rue Gutenberg, 06000, Nice, France
| | - Emilie Aubin
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Laboratoire Génome et Développement des Plantes-UMR CNRS/UPVD 5096, Université de Perpignan, 66860, Perpignan, France
| | - Richard Christen
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paola Furla
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France
| | - Didier Forcioli
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
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18
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Kess T, Boulding EG. Genome-wide association analyses reveal polygenic genomic architecture underlying divergent shell morphology in Spanish Littorina saxatilis ecotypes. Ecol Evol 2019; 9:9427-9441. [PMID: 31534666 PMCID: PMC6745682 DOI: 10.1002/ece3.5378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022] Open
Abstract
Gene flow between diverging populations experiencing dissimilar ecological conditions can theoretically constrain adaptive evolution. To minimize the effect of gene flow, alleles underlying traits essential for local adaptation are predicted to be located in linked genome regions with reduced recombination. Local reduction in gene flow caused by selection is expected to produce elevated divergence in these regions. The highly divergent crab-adapted and wave-adapted ecotypes of the marine snail Littorina saxatilis present a model system to test these predictions. We used genome-wide association (GWA) analysis of geometric morphometric shell traits associated with microgeographic divergence between the two L. saxatilis ecotypes within three separate sampling sites. A total of 477 snails that had individual geometric morphometric data and individual genotypes at 4,066 single nucleotide polymorphisms (SNPs) were analyzed using GWA methods that corrected for population structure among the three sites. This approach allowed dissection of the genomic architecture of shell shape divergence between ecotypes across a wide geographic range, spanning two glacial lineages. GWA revealed 216 quantitative trait loci (QTL) with shell size or shape differences between ecotypes, with most loci explaining a small proportion of phenotypic variation. We found that QTL were evenly distributed across 17 linkage groups, and exhibited elevated interchromosomal linkage, suggesting a genome-wide response to divergent selection on shell shape between the two ecotypes. Shell shape trait-associated loci showed partial overlap with previously identified outlier loci under divergent selection between the two ecotypes, supporting the hypothesis of diversifying selection on these genomic regions. These results suggest that divergence in shell shape between the crab-adapted and wave-adapted ecotypes is produced predominantly by a polygenic genomic architecture with positive linkage disequilibrium among loci of small effect.
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Affiliation(s)
- Tony Kess
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
- Present address:
Fisheries and Oceans CanadaSt. John'sNLCanada
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