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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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Harper KE, Scheinberg LA, Boyer KE, Sotka EE. Global distribution of cryptic native, introduced and hybrid lineages in the widespread estuarine amphipod Ampithoe valida. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01452-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Lobov AA, Babkina IY, Danilov LG, Masharskiy AE, Predeus AV, Mikhailova NA, Granovitch AI, Maltseva AL. Species-Specific Proteins in the Oviducts of Snail Sibling Species: Proteotranscriptomic Study of Littorina fabalis and L. obtusata. BIOLOGY 2021; 10:biology10111087. [PMID: 34827080 PMCID: PMC8614816 DOI: 10.3390/biology10111087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 01/08/2023]
Abstract
Genus Littorina subgenus Neritrema (Mollusca, Caenogastropoda) includes the "obtusata" group of closely related species (Littorina obtusata and L. fabalis). The anatomy of the adult reproductive system (pallial oviduct) is the only reliable feature used for species identification in females of these species. Reproductive system anatomy and reproduction-associated proteins often diverge between sibling species. Despite being of high evolutionary interest, the molecular basis of this divergence remains poorly understood. We performed proteotranscriptomic comparison of oviducts of L. obtusata and L. fabalis by RNA-seq on Illumina HiSeq 2500 and two-dimensional protein electrophoresis (2D DIGE) with MS/MS identification of the species-specific proteins. The interspecies differences in the oviduct were associated with (1) metabolic proteins reflecting overall physiological differences between L. obtusata and L. fabalis, (2) receptor proteins, and (3) transcripts related to transposable elements (TEs). Various receptors identified may recognize a wide variety of ligands from pathogen-associated molecular patterns to specific carbohydrates on the sperm surface. Therefore, these may participate in immune defense as well as in sperm storage and regulation. Species-specificity of multiple TE sequences (coding for reverse transcriptase and ribonuclease H) may indicate the important role of these genomic elements in the Littorina species divergence, which has not been reported previously.
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Affiliation(s)
- Arseniy A. Lobov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.Y.B.); (A.I.G.); (A.L.M.)
- Laboratory of Regenerative Biomedicine, Institute of Cytology of the RAS, 194064 St. Petersburg, Russia
- Correspondence: or
| | - Irina Y. Babkina
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.Y.B.); (A.I.G.); (A.L.M.)
| | - Lavrentii G. Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Alexey E. Masharskiy
- Core Facility Center, “Development of Molecular and Cell Technologies” and “Biobank”, St. Petersburg State University, 198504 St. Petersburg, Russia;
| | | | - Natalia A. Mikhailova
- Centre of Cell Technologies, Institute of Cytology of the RAS, 194064 St. Petersburg, Russia;
| | - Andrei I. Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.Y.B.); (A.I.G.); (A.L.M.)
| | - Arina L. Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.Y.B.); (A.I.G.); (A.L.M.)
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4
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Baptista L, Meimberg H, Ávila SP, Santos AM, Curto M. Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago. BMC Ecol Evol 2021; 21:128. [PMID: 34157972 PMCID: PMC8218459 DOI: 10.1186/s12862-021-01862-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022] Open
Abstract
Background In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics. Results Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands. Conclusions Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01862-1.
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Affiliation(s)
- L Baptista
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. .,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801, Ponta Delgada, Azores, Portugal. .,MPB-Marine Palaeontology and Biogeography Lab, Universidade Dos Açores, 9501-801, Ponta Delgada, Azores, Portugal. .,Faculdade de Ciências da Universidade do Porto, Rua Do Campo Alegre, 1021/1055, 4169-007, Porto, Portugal.
| | - H Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - S P Ávila
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801, Ponta Delgada, Azores, Portugal.,MPB-Marine Palaeontology and Biogeography Lab, Universidade Dos Açores, 9501-801, Ponta Delgada, Azores, Portugal.,Faculdade de Ciências da Universidade do Porto, Rua Do Campo Alegre, 1021/1055, 4169-007, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências e Tecnologia, Universidade Dos Açores, 9501-801, Ponta Delgada, Azores, Portugal
| | - A M Santos
- Faculdade de Ciências da Universidade do Porto, Rua Do Campo Alegre, 1021/1055, 4169-007, Porto, Portugal.,Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, no. 7, 4485-661, Vairão, Portugal
| | - M Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.,MARE, Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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5
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Maltseva AL, Varfolomeeva MA, Lobov AA, Tikanova PO, Repkin EA, Babkina IY, Panova M, Mikhailova NA, Granovitch AI. Premating barriers in young sympatric snail species. Sci Rep 2021; 11:5720. [PMID: 33707514 PMCID: PMC7952697 DOI: 10.1038/s41598-021-84407-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
Sympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (IPC) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and IPC, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.
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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
| | - Arseniy A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - Polina O Tikanova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Egor A Repkin
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - Irina Y Babkina
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - Marina Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - 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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6
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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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Marques JP, Sotelo G, Galindo J, Chaube P, Costa D, Afonso S, Panova M, Nowick K, Butlin R, Hollander J, Faria R. Transcriptomic resources for evolutionary studies in flat periwinkles and related species. Sci Data 2020; 7:73. [PMID: 32127542 PMCID: PMC7054417 DOI: 10.1038/s41597-020-0408-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/29/2020] [Indexed: 12/04/2022] Open
Abstract
The flat periwinkles, Littorina fabalis and L. obtusata, comprise two sister gastropod species that have an enormous potential to elucidate the mechanisms involved in ecological speciation in the marine realm. However, the molecular resources currently available for these species are still scarce. In order to circumvent this limitation, we used RNA-seq data to characterize the transcriptome of four individuals from each species sampled in different locations across the Iberian Peninsula. Four de novo transcriptome assemblies were generated, as well as a pseudo-reference using the L. saxatilis reference transcriptome as backbone. After transcripts' annotation, variant calling resulted in the identification of 19,072 to 45,340 putatively species-diagnostic SNPs. The discriminatory power of a subset of these SNPs was validated by implementing an independent genotyping assay to characterize reference populations, resulting in an accurate classification of individuals into each species and in the identification of hybrids between the two. These data comprise valuable genomic resources for a wide range of evolutionary and conservation studies in flat periwinkles and related taxa.
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Affiliation(s)
- João P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Graciela Sotelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Juan Galindo
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Pragya Chaube
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Diana Costa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Marina Panova
- Department of Marine Sciences, Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Katja Nowick
- Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
| | - Roger Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Marine Sciences, Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Hollander
- Department of Biology, Aquatic Ecology, Lund University, Lund, Sweden
- World Maritime University, Malmö, 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.
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
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8
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Maltseva AL, Varfolomeeva MA, Lobov AA, Tikanova P, Panova M, Mikhailova NA, Granovitch AI. Proteomic similarity of the Littorinid snails in the evolutionary context. PeerJ 2020; 8:e8546. [PMID: 32095363 PMCID: PMC7024583 DOI: 10.7717/peerj.8546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/10/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. METHODS Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation. RESULTS Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of 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
| | - Arseniy A. Lobov
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Polina Tikanova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina Panova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Sweden
| | - 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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9
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Sotelo G, Duvetorp M, Costa D, Panova M, Johannesson K, Faria R. Phylogeographic history of flat periwinkles, Littorina fabalis and L. obtusata. BMC Evol Biol 2020; 20:23. [PMID: 32039690 PMCID: PMC7011314 DOI: 10.1186/s12862-019-1561-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background The flat periwinkles, Littorina fabalis and L. obtusata, are two sister species widely distributed throughout the Northern Atlantic shores with high potential to inform us about the process of ecological speciation in the intertidal. However, whether gene flow has occurred during their divergence is still a matter of debate. A comprehensive assessment of the genetic diversity of these species is also lacking and their main glacial refugia and dispersal barriers remain largely unknown. In order to fill these gaps, we sequenced two mitochondrial genes and two nuclear fragments to perform a phylogeographic analysis of flat periwinkles across their distribution range. Results We identified two main clades largely composed by species-specific haplotypes corresponding to L. obtusata and L. fabalis, with moderate to strong support, respectively. Importantly, a model of divergence with gene flow between the two species (from L. obtusata to L. fabalis) was better supported, both in Iberia and in northern-central Europe. Three mitochondrial clades were detected within L. fabalis and two within L. obtusata, with strong divergence between Iberia and the remaining populations. The largest component of the genetic variance within each species was explained by differences between geographic regions associated with these clades. Our data suggests that overall intraspecific genetic diversity is similar between the two flat periwinkle species and that populations from Iberia tend to be less diverse than populations from northern-central Europe. Conclusions The phylogeographic analysis of this sister-species pair supports divergence with gene flow. This system thus provides us with the opportunity to study the contribution of gene flow and natural selection during diversification. The distribution of the different clades suggests the existence of glacial refugia in Iberia and northern-central Europe for both species, with a main phylogeographic break between these regions. Although the genetic diversity results are not fully conclusive, the lower diversity observed in Iberia could reflect marginal conditions at the southern limit of their distribution range during the current interglacial period.
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Affiliation(s)
- 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, S10 2TN, 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
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - 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, S10 2TN, UK. .,IBE, Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
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10
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Costa D, Sotelo G, Kaliontzopoulou A, Carvalho J, Butlin R, Hollander J, Faria R. Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata. Ecol Evol 2020; 10:1158-1179. [PMID: 32076505 PMCID: PMC7029087 DOI: 10.1002/ece3.5943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/21/2019] [Accepted: 11/27/2019] [Indexed: 01/22/2023] Open
Abstract
Characterizing the patterns of hybridization between closely related species is crucial to understand the role of gene flow in speciation. In particular, systems comprising multiple contacts between sister species offer an outstanding opportunity to investigate how reproductive isolation varies with environmental conditions, demography and geographic contexts of divergence. The flat periwinkles, Littorina obtusata and L. fabalis (Gastropoda), are two intertidal sister species with marked ecological differences compatible with late stages of speciation. Although hybridization between the two was previously suggested, its extent across the Atlantic shores of Europe remained largely unknown. Here, we combined genetic (microsatellites and mtDNA) and morphological data (shell and male genital morphology) from multiple populations of flat periwinkles in north-western Iberia to assess the extent of current and past hybridization between L. obtusata and L. fabalis under two contrasting geographic settings of divergence (sympatry and allopatry). Hybridization signatures based on both mtDNA and microsatellites were stronger in sympatric sites, although evidence for recent extensive admixture was found in a single location. Misidentification of individuals into species based on shell morphology was higher in sympatric than in allopatric sites. However, despite hybridization, species distinctiveness based on this phenotypic trait together with male genital morphology remained relatively high. The observed variation in the extent of hybridization among locations provides a rare opportunity for future studies on the consequences of different levels of gene flow for reinforcement, thus informing about the mechanisms underlying the completion of speciation.
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Affiliation(s)
- Diana Costa
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Department of BiologyFaculty of SciencesUniversity of PortoPortoPortugal
- CIIMARInterdisciplinary Centre of Marine and Environmental ResearchUniversity of PortoPortoPortugal
| | - Graciela Sotelo
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Antigoni Kaliontzopoulou
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - João Carvalho
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- cE3cCentre for Ecology, Evolution and Environmental ChangesDepartamento de Biologia AnimalFaculdade de Ciências da Universidade de LisboaLisbonPortugal
| | - Roger Butlin
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Johan Hollander
- Department of BiologyAquatic Ecology UnitLund UniversityLundSweden
- Global Ocean InstituteWorld Maritime UniversityMalmöSweden
| | - Rui Faria
- CIBIO‐InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- CIIMARInterdisciplinary Centre of Marine and Environmental ResearchUniversity of PortoPortoPortugal
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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11
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Johannesson K, Butlin RK, Panova M, Westram AM. Mechanisms of Adaptive Divergence and Speciation in Littorina saxatilis: Integrating Knowledge from Ecology and Genetics with New Data Emerging from Genomic Studies. POPULATION GENOMICS 2017. [DOI: 10.1007/13836_2017_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Marques JP, Sotelo G, Larsson T, Johannesson K, Panova M, Faria R. Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis. Mar Genomics 2016; 32:41-47. [PMID: 27867038 DOI: 10.1016/j.margen.2016.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/16/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
The flat periwinkles, Littorina fabalis and L. obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L. saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L. saxatilis this problem was overcome with additional long-reads and we were able to assemble the complete mitogenome. Both gene order and nucleotide composition are similar between the three species as well as compared to other Littorinimorpha. A large variance in divergence was observed across mitochondrial regions, with six- to ten-fold difference between the highest and the lowest divergence rates. Based on nucleotide changes on the whole molecule and assuming a molecular clock, L. fabalis and L. obtusata started to diverge around 0.8 Mya (0.4-1.1 Mya). The evolution of the mitochondrial protein-coding genes in the three Littorina species appears mainly influenced by purifying selection as revealed by phylogenetic tests based on dN/dS ratios that did not detect any evidence for positive selection, although some caution is required given the limited power of the dataset and the implemented approaches.
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Affiliation(s)
- João P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Graciela Sotelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Tomas Larsson
- University of Gothenburg, Department of Marine Sciences, Box 460, SE -405 30 Gothenburg, Sweden.
| | - Kerstin Johannesson
- University of Gothenburg, Department of Marine Sciences, Tjärnö, SE -452 96 Strömstad, Sweden.
| | - Marina Panova
- University of Gothenburg, Department of Marine Sciences, Tjärnö, SE -452 96 Strömstad, Sweden.
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; IBE, Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Pompeu Fabra University, Doctor Aiguader 88, 08003 Barcelona, Spain.
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13
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Ardehed A, Johansson D, Sundqvist L, Schagerström E, Zagrodzka Z, Kovaltchouk NA, Bergström L, Kautsky L, Rafajlovic M, Pereyra RT, Johannesson K. Divergence within and among Seaweed Siblings (Fucus vesiculosus and F. radicans) in the Baltic Sea. PLoS One 2016; 11:e0161266. [PMID: 27525655 PMCID: PMC4985153 DOI: 10.1371/journal.pone.0161266] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
Closely related taxa provide significant case studies for understanding evolution of new species but may simultaneously challenge species identification and definition. In the Baltic Sea, two dominant and perennial brown algae share a very recent ancestry. Fucus vesiculosus invaded this recently formed postglacial sea 8000 years ago and shortly thereafter Fucus radicans diverged from this lineage as an endemic species. In the Baltic Sea both species reproduce sexually but also recruit fully fertile new individuals by asexual fragmentation. Earlier studies have shown local differences in morphology and genetics between the two taxa in the northern and western Bothnian Sea, and around the island of Saaremaa in Estonia, but geographic patterns seem in conflict with a single origin of F. radicans. To investigate the relationship between northern and Estonian distributions, we analysed the genetic variation using 9 microsatellite loci in populations from eastern Bothnian Sea, Archipelago Sea and the Gulf of Finland. These populations are located in between earlier studied populations. However, instead of bridging the disparate genetic gap between N-W Bothnian Sea and Estonia, as expected from a simple isolation-by-distance model, the new populations substantially increased overall genetic diversity and showed to be strongly divergent from the two earlier analysed regions, showing signs of additional distinct populations. Contrasting earlier findings of increased asexual recruitment in low salinity in the Bothnian Sea, we found high levels of sexual reproduction in some of the Gulf of Finland populations that inhabit extremely low salinity. The new data generated in this study supports the earlier conclusion of two reproductively isolated but very closely related species. However, the new results also add considerable genetic and morphological complexity within species. This makes species separation at geographic scales more demanding and suggests a need for more comprehensive approaches to further disentangle the intriguing relationship and history of the Baltic Sea fucoids.
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Affiliation(s)
- Angelica Ardehed
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Johansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Sundqvist
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ellen Schagerström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Zuzanna Zagrodzka
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad. Sweden
| | | | - Lena Bergström
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Lena Kautsky
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marina Rafajlovic
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
| | - Ricardo T. Pereyra
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad. Sweden
| | - Kerstin Johannesson
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad. Sweden
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Trivedi S, Aloufi AA, Ansari AA, Ghosh SK. Role of DNA barcoding in marine biodiversity assessment and conservation: An update. Saudi J Biol Sci 2016; 23:161-71. [PMID: 26980996 PMCID: PMC4778524 DOI: 10.1016/j.sjbs.2015.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/09/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.
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Affiliation(s)
- Subrata Trivedi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abdulhadi A. Aloufi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abid A. Ansari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sankar K. Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
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15
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With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast. Sci Rep 2016; 6:20226. [PMID: 26876495 PMCID: PMC4753432 DOI: 10.1038/srep20226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/30/2015] [Indexed: 01/13/2023] Open
Abstract
The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.
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Carvalho J, Sotelo G, Galindo J, Faria R. Genetic characterization of flat periwinkles (Littorinidae) from the Iberian Peninsula reveals interspecific hybridization and different degrees of differentiation. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- João Carvalho
- Departamento de Bioquímica; Xenética e Inmunoloxía; Facultade de Bioloxía; Universidade de Vigo. Campus de Vigo; 36310 Vigo Spain
- Departamento de Biologia Ambiental; Faculdade de Ciências; Universidade de Lisboa. Campo Grande; 1749-016 Lisboa Portugal
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | - Graciela Sotelo
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | - Juan Galindo
- Departamento de Bioquímica; Xenética e Inmunoloxía; Facultade de Bioloxía; Universidade de Vigo. Campus de Vigo; 36310 Vigo Spain
| | - Rui Faria
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
- IBE; Institute of Evolutionary Biology (CSIC-UPF); Department of Experimental and Health Sciences; Pompeu Fabra University. Doctor Aiguader 88; 08003 Barcelona Spain
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Mohrbeck I, Raupach MJ, Martínez Arbizu P, Knebelsberger T, Laakmann S. High-Throughput Sequencing-The Key to Rapid Biodiversity Assessment of Marine Metazoa? PLoS One 2015; 10:e0140342. [PMID: 26479071 PMCID: PMC4610693 DOI: 10.1371/journal.pone.0140342] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/24/2015] [Indexed: 02/03/2023] Open
Abstract
The applications of traditional morphological and molecular methods for species identification are greatly restricted by processing speed and on a regional or greater scale are generally considered unfeasible. In this context, high-throughput sequencing, or metagenetics, has been proposed as an efficient tool to document biodiversity. Here we evaluated the effectiveness of 454 pyrosequencing in marine metazoan community analysis using the 18S rDNA: V1-V2 region. Multiplex pyrosequencing of the V1-V2 region was used to analyze two pooled samples of DNA, one comprising 118 and the other 37 morphologically identified species, and one natural sample taken directly from a North Sea zooplankton community. A DNA reference library comprising all species represented in the pooled samples was created by Sanger sequencing, and this was then used to determine the optimal similarity threshold for species delineation. The optimal threshold was found at 99% species similarity, with 85% identification success. Pyrosequencing was able to identify between fewer species: 67% and 78% of the species in the two pooled samples. Also, a large number of sequences for three species that were not included in the pooled samples were amplified by pyrosequencing, suggesting preferential amplification of some genotypes and the sensitivity of this approach to even low levels of contamination. Conversely, metagenetic analysis of the natural zooplankton sample identified many more species (particularly gelatinous zooplankton and meroplankton) than morphological analysis of a formalin-fixed sample from the same sampling site, suggesting an increased level of taxonomic resolution with pyrosequencing. The study demonstrated that, based on the V1-V2 region, 454 sequencing does not provide accurate species differentiation and reliable taxonomic classification, as it is required in most biodiversity monitoring. The analysis of artificially prepared samples indicated that species detection in pyrosequencing datasets is complicated by potential PCR-based biases and that the V1-V2 marker is poorly resolved for some taxa.
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Affiliation(s)
- Inga Mohrbeck
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Michael J Raupach
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Pedro Martínez Arbizu
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Thomas Knebelsberger
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Silke Laakmann
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
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Zafar FHS, Ayub Z, Begum S, Siddiqui G, Roberts D. Limpets of the genus Cellana (Patellogastropoda) from Pakistan, North Arabian Sea: species identification based on DNA sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2868-72. [PMID: 26065851 DOI: 10.3109/19401736.2015.1053133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The true limpets are found in the intertidal zone of the rocky shores of Pakistan, North Arabian Sea. Partial sequence of the mitochondrial cytochrome oxidase I was used to estimate the degree of genetic differentiation among the morphological forms of Cellana, which were considered as three separate species earlier in Pakistan. The study revealed that the three morphs of Cellana on COI sequence generated a single haplotype and matched with the COI sequence of Cellana karachiensis. This point out the phenotypic plasticity between the proposed species.
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Affiliation(s)
| | - Zarrien Ayub
- b Centre of Excellence in Marine Biology, University of Karachi , Karachi , Pakistan , and
| | - Samar Begum
- b Centre of Excellence in Marine Biology, University of Karachi , Karachi , Pakistan , and
| | - Ghazala Siddiqui
- b Centre of Excellence in Marine Biology, University of Karachi , Karachi , Pakistan , and
| | - David Roberts
- c C-Mar School of Biological Sciences, Queen's University Belfast , Belfast , UK
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Panova M, Johansson T, Canbäck B, Bentzer J, Rosenblad MA, Johannesson K, Tunlid A, André C. Species and gene divergence in Littorina snails detected by array comparative genomic hybridization. BMC Genomics 2014; 15:687. [PMID: 25135785 PMCID: PMC4148934 DOI: 10.1186/1471-2164-15-687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/11/2014] [Indexed: 12/11/2022] Open
Abstract
Background Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis. Results We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. Conclusions The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Panova
- Department of Biological and Environmental Sciences - Tjärnö, Gothenburg University, Gothenburg, Sweden.
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Micro-spatial distribution of two sibling periwinkle species across the intertidal indicates hybrdization. Genetica 2013; 141:293-301. [PMID: 23887893 DOI: 10.1007/s10709-013-9728-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Abstract
Populations of periwinkles Littorina saxatilis (Olivi 1792) and L. arcana Hannaford Ellis, 1978 are well suited for microevolutionary studies, being at the same time closely related and intraspecifically diverse. The divergence between these two sibling species, sympatric over large parts of their distribution areas, is small, the only morphological difference being the pallial gland complex structure in females. Molecular identification is possible with the use of a RAPD nuclear marker (cloned A2.8 DNA fragment) typical for L. arcana. However, in some individuals from sympatric populations molecular and morphological criteria suggest conflicting species affiliation, which may be explained either by hybridization or by shared ancestral polymorphism. We tested the hybridization hypotheses examining the micro-spatial distribution of these two species across the intertidal zone in two distant sites at the Barents Sea. We found that (a) the frequency of putative hybrids in sympatric populations was proportional to the frequency of L. arcana; (b) L. saxatilis bearing A2.8 DNA fragment were almost absent in the lower part of the intertidal zone, where L. arcana was absent too; (c) there was a close positive correlation between the distribution of potential parent molluscs and putative hybrids. Moreover, logistic regression models showed a good agreement between the distribution of putative hybrid frequencies and that of parental species frequencies. All our observations taken together support the hypothesis of hybridization between L. saxatilis and L. arcana. Elucidating the mechanisms that support the species status of these sympatric populations is necessary.
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Ng TPT, Saltin SH, Davies MS, Johannesson K, Stafford R, Williams GA. Snails and their trails: the multiple functions of trail-following in gastropods. Biol Rev Camb Philos Soc 2013; 88:683-700. [DOI: 10.1111/brv.12023] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 01/04/2013] [Accepted: 01/07/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Terence P. T. Ng
- The Swire Institute of Marine Science and School of Biological Sciences; The University of Hong Kong; Hong Kong SAR; China
| | - Sara H. Saltin
- Department of Biological and Environmental Sciences-Tjärnö; University of Gothenburg; SE-452 96; Strömstad; Sweden
| | - Mark S. Davies
- Faculty of Applied Sciences; University of Sunderland; Sunderland; SR1 3SD; UK
| | - Kerstin Johannesson
- Department of Biological and Environmental Sciences-Tjärnö; University of Gothenburg; SE-452 96; Strömstad; Sweden
| | - Richard Stafford
- Institute of Biomedical and Environmental Science and Technology (iBEST); University of Bedfordshire; Luton; LU1 3JU; UK
| | - Gray A. Williams
- The Swire Institute of Marine Science and School of Biological Sciences; The University of Hong Kong; Hong Kong SAR; China
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Reid DG, Dyal P, Williams ST. A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2011.00505.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Doellman MM, Trussell GC, Grahame JW, Vollmer SV. Phylogeographic analysis reveals a deep lineage split within North Atlantic Littorina saxatilis. Proc Biol Sci 2011; 278:3175-83. [PMID: 21429920 DOI: 10.1098/rspb.2011.0346] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogeographic studies provide critical insight into the evolutionary histories of model organisms; yet, to date, range-wide data are lacking for the rough periwinkle Littorina saxatilis, a classic example of marine sympatric speciation. Here, we use mitochondrial DNA (mtDNA) sequence data to demonstrate that L. saxatilis is not monophyletic for this marker, but is composed of two distinct mtDNA lineages (I and II) that are shared with sister species Littorina arcana and Littorina compressa. Bayesian coalescent dating and phylogeographic patterns indicate that both L. saxatilis lineages originated in the eastern North Atlantic, around the British Isles, at approximately 0.64 Ma. Both lineages are now distributed broadly across the eastern, central and western North Atlantic, and show strong phylogeographic structure among regions. The Iberian Peninsula is genetically distinct, suggesting prolonged isolation from northeastern North Atlantic populations. Western North Atlantic populations of L. saxatilis lineages I and II predate the last glacial maximum and have been isolated from eastern North Atlantic populations since that time. This identification of two distinct, broadly distributed mtDNA lineages further complicates observed patterns of repeated incipient ecological speciation in L. saxatilis, because the sympatric origins of distinct ecotype pairs on eastern North Atlantic shores may be confounded by admixture of divergent lineages.
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Abstract
More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
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Affiliation(s)
- Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
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Intron sequences of arginine kinase in an intertidal snail suggest an ecotype-specific selective sweep and a gene duplication. Heredity (Edinb) 2010; 106:808-16. [PMID: 20877396 DOI: 10.1038/hdy.2010.123] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Many species with restricted gene flow repeatedly respond similarly to local selection pressures. To fully understand the genetic mechanisms behind this process, the phylogeographic history of the species (inferred from neutral markers) as well as the loci under selection need to be known. Here we sequenced an intron in the arginine kinase gene (Ark), which shows strong clinal variation between two locally adapted ecotypes of the flat periwinkle, Littorina fabalis. The 'small-sheltered' ecotype was almost fixed for one haplotype, H1, in populations on both sides of the North Sea, unlike the 'large-moderately exposed ecotype', which segregated for ten different haplotypes. This contrasts with neutral markers, where the two ecotypes are equally variable. H1 could have been driven to high frequency in an ancestral population and then repeatedly spread to sheltered habitats due to local selection pressures with the colonization of both sides of the North Sea, after the last glacial maximum (~18 000 years ago). An alternative explanation is that a positively selected mutation, in or linked to Ark, arose after the range expansion and secondarily spread through sheltered populations throughout the distribution range, causing this ecotype to evolve in a concerted fashion. Also, we were able to sequence up to four haplotypes consistently from some individuals, suggesting a gene duplication in Ark.
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Rugman-Jones PF, Hoddle MS, Stouthamer R. Nuclear-mitochondrial barcoding exposes the global pest Western flower thrips (Thysanoptera: Thripidae) as two sympatric cryptic species in its native California. JOURNAL OF ECONOMIC ENTOMOLOGY 2010; 103:877-886. [PMID: 20568635 DOI: 10.1603/ec09300] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Over the past three decades, Western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), has become a major worldwide pest of many agricultural and horticultural crops. In response, much time, money, and effort have been put into pure and applied research focusing on the biology and control of this pest. Western flower thrips is native to Western North America and widespread in California. High levels of variation in basic biology, pest status, and resistance to insecticides bring into question the specific status of Western flower thrips. We used nuclear-mitochondrial barcoding to compare DNA sequences of nuclear and mitochondrial genes between Western flower thrips populations across California, looking for association between these unlinked loci. Sequences of D2 domain of 28S and cytochrome c oxidase I gene revealed the existence of two distinct but sympatric genetic entities, and we describe a simple polymerase chain reaction-based method for diagnosing these entities. The complete association of these nuclear and mitochondrial loci in areas of sympatry is indicative of reproductive isolation and the existence of two cryptic species, both of which key out to Western flower thrips by using morphological characters. The finding that Western flower thrips is a complex of two species has important implications for past, current, and most importantly future research on these pests.
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Affiliation(s)
- Paul F Rugman-Jones
- Department of Entomology, University of California, Riverside, CA 92521, USA.
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