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Santos CA, Sonoda GG, Cortez T, Coutinho LL, Andrade SCS. Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation. Genome Biol Evol 2021; 13:6171147. [PMID: 33720344 PMCID: PMC8070887 DOI: 10.1093/gbe/evab050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.
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Affiliation(s)
- Camilla A Santos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriel G Sonoda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz L Coutinho
- Departamento de Ciência Animal, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, São Paulo, SP, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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Iannucci A, Cannicci S, Caliani I, Baratti M, Pretti C, Fratini S. Investigation of mechanisms underlying chaotic genetic patchiness in the intertidal marbled crab Pachygrapsus marmoratus (Brachyura: Grapsidae) across the Ligurian Sea. BMC Evol Biol 2020; 20:108. [PMID: 32831022 PMCID: PMC7444255 DOI: 10.1186/s12862-020-01672-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 08/11/2020] [Indexed: 12/25/2022] Open
Abstract
Background Studies on marine community dynamics and population structures are limited by the lack of exhaustive knowledge on the larval dispersal component of connectivity. Genetic data represents a powerful tool in understanding such processes in the marine realm. When dealing with dispersion and connectivity in marine ecosystems, many evidences show patterns of genetic structure that cannot be explained by any clear geographic trend and may show temporal instability. This scenario is usually referred to as chaotic genetic patchiness, whose driving mechanisms are recognized to be selection, temporal shifts in local population dynamics, sweepstakes reproductive success and collective dispersal. In this study we focused on the marbled crab Pachygrapsus marmoratus that inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean, and disperses through planktonic larvae for about 1 month. P. marmoratus exhibits unexpectedly low connectivity levels at local scale, although well-defined phylogeographic patterns across the species’ distribution range were described. This has been explained as an effect of subtle geographic barriers or due to sweepstake reproductive success. In order to verify a chaotic genetic patchiness scenario, and to explore mechanisms underlying it, we planned our investigation within the Ligurian Sea, an isolated basin of the western Mediterranean Sea, and we genotyped 321 individuals at 11 microsatellite loci. Results We recorded genetic heterogeneity among our Ligurian Sea samples with the occurrence of genetic clusters not matching the original populations and a slight inter-population divergence, with the geographically most distant populations being the genetically most similar ones. Moreover, individuals from each site were assigned to all the genetic clusters. We also recorded evidences of self-recruitment and a higher than expected within-site kinship. Conclusions Overall, our results suggest that the chaotic genetic patchiness we found in P. marmoratus Ligurian Sea populations is the result of a combination of differences in reproductive success, en masse larval dispersion and local larval retention. This study defines P. marmoratus as an example of marine spawner whose genetic pool is not homogenous at population level, but rather split in a chaotic mosaic of slightly differentiated genetic patches derived from complex and dynamic ecological processes.
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Affiliation(s)
- A Iannucci
- Department of Biology, University of Florence, via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - S Cannicci
- Department of Biology, University of Florence, via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy. .,The Swire Institute of Marine Science and the Division of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR.
| | - I Caliani
- Department of Environment, Earth and Physical Sciences, University of Siena, via Mattioli 4, 53100, Siena, Italy
| | - M Baratti
- National Research Council - IBBR, via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - C Pretti
- Interuniversity Consortium of Marine Biology of Leghorn "G. Bacci", viale N. Sauro 4, 57128, Livorno, Italy.,Department of Veterinary Sciences, University of Pisa, via Livornese lato monte, 56122, San Piero a Grado (PI), Italy
| | - S Fratini
- Department of Biology, University of Florence, via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
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Clark MS, Thorne MAS, King M, Hipperson H, Hoffman JI, Peck LS. Life in the intertidal: Cellular responses, methylation and epigenetics. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13077] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Melody S. Clark
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| | | | - Michelle King
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of Sheffield Sheffield UK
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of Bielefeld Bielefeld Germany
| | - Lloyd S. Peck
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
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Eldon B, Riquet F, Yearsley J, Jollivet D, Broquet T. Current hypotheses to explain genetic chaos under the sea. Curr Zool 2016; 62:551-566. [PMID: 29491945 PMCID: PMC5829445 DOI: 10.1093/cz/zow094] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/27/2016] [Indexed: 01/07/2023] Open
Abstract
Chaotic genetic patchiness (CGP) refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns: selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.
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Affiliation(s)
- Bjarki Eldon
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und
Biodiversitätsforschung, Berlin 10115, Germany
| | - Florentine Riquet
- Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5,
France
- ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète 34200, France
| | - Jon Yearsley
- School of Biology and Environmental Science and UCD Earth Institute,
University College Dublin, Belfield, Dublin 4, Ireland
| | - Didier Jollivet
- Centre National de la Recherche Scientifique, Team Adaptation and Biology of
Invertebrates in Extreme Environments, Station Biologique de Roscoff, Roscoff 29680,
France
- Sorbonne Universités, Université Pierre et Marie Curie, Unité Mixte de
Recherche 7144, Station Biologique de Roscoff, Roscoff 29680, France
| | - Thomas Broquet
- Sorbonne Universités, Université Pierre et Marie Curie, Unité Mixte de
Recherche 7144, Station Biologique de Roscoff, Roscoff 29680, France
- Centre National de la Recherche Scientifique, Team Diversity and
Connectivity of Coastal Marine Landscapes, Station Biologique de Roscoff, Roscoff 29680,
France
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Abstract
The marine snail Littorina saxatilis is a common inhabitant of intertidal shores of the north Atlantic. It is amazingly polymorphic and forms reproductively isolated ecotypes in microhabitats where crabs are either present and wave action is less furious, or where waves are strong and crabs are absent. Decades of research have unveiled much of the ecological and demographic context of the formation of crab‐ and wave‐ecotype snails showing important phenotypic differences being inherited, differential selection being strong over adjacent microhabitats, local dispersal being restricted, and long‐distance transports of individuals being rare. In addition, strong assortative mating of ecotypes has been shown to include a component of male mate preference based on female size. Several studies support ecotypes being diverged locally and under gene flow in a parallel and highly replicated fashion. The high level of replication at various levels of independence (from local to pan‐European scale) provides excellent opportunities to investigate the detailed mechanisms of microevolution, including the formation of barriers to gene flow. Current investigations benefit from a draft reference genome and an integration of genomic approaches, modelling and experiments to unveil molecular and ecological components of speciation and their interactions.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences - Tjärnö University of Gothenburg Strömstad Sweden
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Johannesson K, Panova M, Kemppainen P, André C, Rolán-Alvarez E, Butlin RK. Repeated evolution of reproductive isolation in a marine snail: unveiling mechanisms of speciation. Philos Trans R Soc Lond B Biol Sci 2010; 365:1735-47. [PMID: 20439278 DOI: 10.1098/rstb.2009.0256] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Distinct ecotypes of the snail Littorina saxatilis, each linked to a specific shore microhabitat, form a mosaic-like pattern with narrow hybrid zones in between, over which gene flow is 10-30% of within-ecotype gene flow. Multi-locus comparisons cluster populations by geographic affinity independent of ecotype, while loci under selection group populations by ecotype. The repeated occurrence of partially reproductively isolated ecotypes and the conflicting patterns in neutral and selected genes can either be explained by separation in allopatry followed by secondary overlap and extensive introgression that homogenizes neutral differences evolved under allopatry, or by repeated evolution in parapatry, or in sympatry, with the same ecotypes appearing in each local site. Data from Spain, the UK and Sweden give stronger support for a non-allopatric model of ecotype formation than for an allopatric model. Several different non-allopatric mechanisms can, however, explain the repeated evolution of the ecotypes: (i) parallel evolution by new mutations in different populations; (ii) evolution from standing genetic variation; and (iii) evolution in concert with rapid spread of new positive mutations among populations inhabiting similar environments. These models make different predictions that can be tested using comprehensive phylogenetic information combined with candidate loci sequencing.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Ecology-Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden.
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Intense habitat-specific fisheries-induced selection at the molecular Pan I locus predicts imminent collapse of a major cod fishery. PLoS One 2009; 4:e5529. [PMID: 19479037 PMCID: PMC2682699 DOI: 10.1371/journal.pone.0005529] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 03/27/2009] [Indexed: 11/19/2022] Open
Abstract
Predation is a powerful agent in the ecology and evolution of predator and prey. Prey may select multiple habitats whereby different genotypes prefer different habitats. If the predator is also habitat-specific the prey may evolve different habitat occupancy. Drastic changes can occur in the relation of the predator to the evolved prey. Fisheries exert powerful predation and can be a potent evolutionary force. Fisheries-induced selection can lead to phenotypic changes that influence the collapse and recovery of the fishery. However, heritability of the phenotypic traits involved and selection intensities are low suggesting that fisheries-induced evolution occurs at moderate rates at decadal time scales. The Pantophysin I (Pan I) locus in Atlantic cod (Gadus morhua), representing an ancient balanced polymorphism predating the split of cod and its sister species, is under an unusual mix of balancing and directional selection including current selective sweeps. Here we show that Pan I alleles are highly correlated with depth with a gradient of 0.44% allele frequency change per meter. AA fish are shallow-water and BB deep-water adapted in accordance with behavioral studies using data storage tags showing habitat selection by Pan I genotype. AB fish are somewhat intermediate although closer to AA. Furthermore, using a sampling design covering space and time we detect intense habitat-specific fisheries-induced selection against the shallow-water adapted fish with an average 8% allele frequency change per year within year class. Genotypic fitness estimates (0.08, 0.27, 1.00 of AA, AB, and BB respectively) predict rapid disappearance of shallow-water adapted fish. Ecological and evolutionary time scales, therefore, are congruent. We hypothesize a potential collapse of the fishery. We find that probabilistic maturation reaction norms for Atlantic cod at Iceland show declining length and age at maturing comparable to changes that preceded the collapse of northern cod at Newfoundland, further supporting the hypothesis. We speculate that immediate establishment of large no-take reserves may help avert collapse.
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