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Thomas-Bulle C, Bertrand D, Nagarajan N, Copley RR, Corre E, Hourdez S, Bonnivard É, Claridge-Chang A, Jollivet D. Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella. BMC Ecol Evol 2022; 22:106. [PMID: 36057769 PMCID: PMC9441076 DOI: 10.1186/s12862-022-02057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promoting local adaptation and contributing to bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution. Results We explored genomic patterns of divergence in the early and late stages of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.
Conclusion Our analyses highlight the non-negligible role of natural selection on both the early and late stages of speciation in the iconic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed light on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02057-y.
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Rodríguez-Flores P, Macpherson E, Schnabel K, Ahyong S, Corbari L, Machordom A. Depth as a driver of evolution and diversification of ancient squat lobsters (Decapoda, Galatheoidea, Phylladiorhynchus). Mol Phylogenet Evol 2022; 171:107467. [DOI: 10.1016/j.ympev.2022.107467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 03/09/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
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Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. J Evol Biol 2021; 34:4-15. [PMID: 33460491 DOI: 10.1111/jeb.13756] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 12/28/2022]
Abstract
Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model-based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.
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Affiliation(s)
- Rui Faria
- 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, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Kerstin Johannesson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,IST Austria, Klosterneuburg, Austria
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Schreiber D, Pfenninger M. Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation. Evol Lett 2021; 5:86-100. [PMID: 33552538 PMCID: PMC7857304 DOI: 10.1002/evl3.204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/11/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022] Open
Abstract
Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component-based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence-simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.
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Affiliation(s)
- Dennis Schreiber
- Department of Molecular EcologySenckenberg Biodiversity and Climate Research CentreFrankfurt am Main60325Germany
- Institute for Molecular and Organismic EvolutionJohannes Gutenberg UniversityMainz55128Germany
| | - Markus Pfenninger
- Department of Molecular EcologySenckenberg Biodiversity and Climate Research CentreFrankfurt am Main60325Germany
- Institute for Molecular and Organismic EvolutionJohannes Gutenberg UniversityMainz55128Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am Main60325Germany
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Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian P, Qiu J. Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific. Evol Appl 2018; 11:1915-1930. [PMID: 30459838 PMCID: PMC6231483 DOI: 10.1111/eva.12696] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 01/09/2023] Open
Abstract
Studying population genetics of deep-sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis-based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co-occurrence of two cryptic semi-isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S-OT) and those in the middle OT (M-OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S-OT and the M-OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S-OT represents a possible contact zone for individuals in the OT-SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai-yon Yonaguni Knoll in the S-OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific.
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Affiliation(s)
- Ting Xu
- Department of BiologyHong Kong Baptist UniversityHong KongChina
| | - Jin Sun
- Department of Ocean ScienceHong Kong University of Science and TechnologyHong KongChina
| | - Hiromi K. Watanabe
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Chong Chen
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Masako Nakamura
- School of Marine Science and TechnologyTokai UniversityShizuokaJapan
| | - Rubao Ji
- Department of BiologyWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Dong Feng
- CAS Key Laboratory of Ocean and Marginal Sea GeologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Jia Lv
- Ministry of Education Key Laboratory of Marine Genetics and BreedingCollege of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and BreedingCollege of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and BreedingCollege of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Pei‐Yuan Qian
- Department of Ocean ScienceHong Kong University of Science and TechnologyHong KongChina
| | - Jian‐Wen Qiu
- Department of BiologyHong Kong Baptist UniversityHong KongChina
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Fourie G, Van der Merwe NA, Wingfield BD, Bogale M, Wingfield MJ, Steenkamp ET. Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex. IMA Fungus 2018; 9:37-48. [PMID: 30018871 PMCID: PMC6048563 DOI: 10.5598/imafungus.2018.09.01.04] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/18/2018] [Indexed: 01/31/2023] Open
Abstract
The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.
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Affiliation(s)
- Gerda Fourie
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicolaas A Van der Merwe
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Mesfin Bogale
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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De Groote A, Hauquier F, Vanreusel A, Derycke S. Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea. BMC Evol Biol 2017; 17:154. [PMID: 28668078 PMCID: PMC5494145 DOI: 10.1186/s12862-017-1003-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/21/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. RESULTS Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. CONCLUSIONS The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.
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Affiliation(s)
- Annelies De Groote
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Freija Hauquier
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
- Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, 1000 Brussels, Belgium
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8
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Breusing C, Vrijenhoek RC, Reusch TBH. Widespread introgression in deep-sea hydrothermal vent mussels. BMC Evol Biol 2017; 17:13. [PMID: 28086786 PMCID: PMC5237248 DOI: 10.1186/s12862-016-0862-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 11/29/2022] Open
Abstract
Background The analysis of hybrid zones is crucial for gaining a mechanistic understanding of the process of speciation and the maintenance of species boundaries. Hybrid zones have been studied intensively in terrestrial and shallow-water ecosystems, but very little is known about their occurrence in deep-sea environments. Here we used diagnostic, single nucleotide polymorphisms in combination with one mitochondrial gene to re-examine prior hypotheses about a contact zone involving deep-sea hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis, living along the Mid-Atlantic Ridge. Results Admixture was found to be asymmetric with respect to the parental species, while introgression was more widespread geographically than previously recognized. Admixed individuals with a majority of alleles from one of the parental species were most frequent in habitats corresponding to that species. Mussels found at a geographically intermediate vent field constituted a genetically mixed population that showed no evidence for hybrid incompatibilities, a finding that does not support a previously inferred tension zone model. Conclusions Our analyses indicate that B. azoricus and B. puteoserpentis hybridize introgressively across a large geographic area without evidence for general hybrid incompatibilities. While these findings shed new light onto the genetic structure of this hybrid zone, many aspects about its nature still remain obscure. Our study sets a baseline for further research that should primarily focus on the acquisition of additional mussel samples and environmental data, a detailed exploration of vent areas and hidden populations as well as genomic analyses in both mussel hosts and their bacterial symbionts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0862-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Corinna Breusing
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany. .,Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA.
| | - Robert C Vrijenhoek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Thorsten B H Reusch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany
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Tobler M, Passow CN, Greenway R, Kelley JL, Shaw JH. The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032418] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydrogen sulfide (H2S) is a respiratory toxicant that creates extreme environments tolerated by few organisms. H2S is also produced endogenously by metazoans and plays a role in cell signaling. The mechanisms of H2S toxicity and its physiological functions serve as a basis to discuss the multifarious strategies that allow animals to survive in H2S-rich environments. Despite their toxicity, H2S-rich environments also provide ecological opportunities, and complex selective regimes of covarying abiotic and biotic factors drive trait evolution in organisms inhabiting H2S-rich environments. Furthermore, adaptation to H2S-rich environments can drive speciation, giving rise to biodiversity hot spots with high levels of endemism in deep-sea hydrothermal vents, cold seeps, and freshwater sulfide springs. The diversity of H2S-rich environments and their inhabitants provides ideal systems for comparative studies of the effects of a clear-cut source of selection across vast geographic and phylogenetic scales, ultimately informing our understanding of how environmental stressors affect ecological and evolutionary processes.
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Affiliation(s)
- Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | | | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jennifer H. Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078
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10
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Breusing C, Johnson SB, Tunnicliffe V, Vrijenhoek RC. Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus septemdierum complex. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0750-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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11
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Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico. PLoS One 2015; 10:e0118460. [PMID: 25859657 PMCID: PMC4393317 DOI: 10.1371/journal.pone.0118460] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/17/2015] [Indexed: 11/19/2022] Open
Abstract
Hydrocarbon seepage is widespread and patchy in the Gulf of Mexico, and six species of symbiont containing bathymodiolin mussels are found on active seeps over wide and overlapping depth and geographic ranges. We use mitochondrial genes to discriminate among the previously known and a newly discovered species and to assess the connectivity among populations of the same species in the northern Gulf of Mexico (GoM). Our results generally validate the morphologically based distribution of the three previously known GoM species of Bathymodiolus, although we found that approximately 10% of the morphologically based identifications were incorrect and this resulted in some inaccuracies with respect to their previously assigned depth and geographical distribution patterns. These data allowed us to confirm that sympatry of two species of Bathymodiolus within a single patch of mussels is common. A new species of bathymodiolin, Bathymodiolus sp. nov., closely related to B. heckerae was also discovered. The two species live at the same depths but have not been found in sympatry and both have small effective population sizes. We found evidence for genetic structure within populations of the three species of Bathymodiolinae for which we had samples from multiple sites and suggest limited connectivity for populations at some sites. Despite relatively small sample sizes, genetic diversity indices suggest the largest population sizes for B. childressi and Tamu fisheri and the smallest for B. heckerae and B. sp. nov. among the GoM bathymodiolins. Moreover, we detected an excess of rare variants indicating recent demographic changes and population expansions for the four species of bathymodiolins from the Gulf of Mexico.
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Wentrup C, Wendeberg A, Schimak M, Borowski C, Dubilier N. Forever competent: deep‐sea bivalves are colonized by their chemosynthetic symbionts throughout their lifetime. Environ Microbiol 2014; 16:3699-713. [DOI: 10.1111/1462-2920.12597] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 08/08/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Cecilia Wentrup
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Annelie Wendeberg
- Department of Environmental Microbiology UFZ, Helmholtz Centre for Environmental Research Permoserstrasse 15 Leipzig 04318 Germany
| | - Mario Schimak
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Christian Borowski
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Nicole Dubilier
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
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13
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The Complete Amino Acid Sequence and Enzymatic Properties of an i-Type Lysozyme Isolated from the Common Orient Clam (Meretrix lusoria). Biosci Biotechnol Biochem 2014; 77:2269-77. [DOI: 10.1271/bbb.130534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Plouviez S, Faure B, Le Guen D, Lallier FH, Bierne N, Jollivet D. A new barrier to dispersal trapped old genetic clines that escaped the Easter Microplate tension zone of the Pacific vent mussels. PLoS One 2013; 8:e81555. [PMID: 24312557 PMCID: PMC3846894 DOI: 10.1371/journal.pone.0081555] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 10/21/2013] [Indexed: 11/23/2022] Open
Abstract
Comparative phylogeography of deep-sea hydrothermal vent species has uncovered several genetic breaks between populations inhabiting northern and southern latitudes of the East Pacific Rise. However, the geographic width and position of genetic clines are variable among species. In this report, we further characterize the position and strength of barriers to gene flow between populations of the deep-sea vent mussel Bathymodiolus thermophilus. Eight allozyme loci and DNA sequences of four nuclear genes were added to previously published sequences of the cytochrome c oxidase subunit I gene. Our data confirm the presence of two barriers to gene flow, one located at the Easter Microplate (between 21°33′S and 31°S) recently described as a hybrid zone, and the second positioned between 7°25′S and 14°S with each affecting different loci. Coalescence analysis indicates a single vicariant event at the origin of divergence between clades for all nuclear loci, although the clines are now spatially discordant. We thus hypothesize that the Easter Microplate barrier has recently been relaxed after a long period of isolation and that some genetic clines have escaped the barrier and moved northward where they have subsequently been trapped by a reinforcing barrier to gene flow between 7°25′S and 14°S.
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Affiliation(s)
- Sophie Plouviez
- Université Pierre et Marie Curie-Paris 6, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- CNRS UMR 7144, Station Biologique de Roscoff, Roscoff, France
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
- * E-mail:
| | - Baptiste Faure
- Université Pierre et Marie Curie-Paris 6, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- CNRS UMR 7144, Station Biologique de Roscoff, Roscoff, France
- Université Montpellier 2, Montpellier, France
- CNRS UMR 5554, Institut des Sciences de l’Evolution, Station Méditerranéenne de l’Environnement Littoral, Sète, France
| | - Dominique Le Guen
- Université Pierre et Marie Curie-Paris 6, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- CNRS UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - François H. Lallier
- Université Pierre et Marie Curie-Paris 6, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- CNRS UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Bierne
- Université Montpellier 2, Montpellier, France
- CNRS UMR 5554, Institut des Sciences de l’Evolution, Station Méditerranéenne de l’Environnement Littoral, Sète, France
| | - Didier Jollivet
- Université Pierre et Marie Curie-Paris 6, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- CNRS UMR 7144, Station Biologique de Roscoff, Roscoff, France
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15
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Multilocus analysis of divergence and introgression in sympatric and allopatric sibling species of the Lutzomyia longipalpis complex in Brazil. PLoS Negl Trop Dis 2013; 7:e2495. [PMID: 24147172 PMCID: PMC3798421 DOI: 10.1371/journal.pntd.0002495] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 09/08/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones. METHODOLOGY/PRINCIPAL FINDINGS We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species. CONCLUSIONS/SIGNIFICANCE The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil.
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Lorion J, Kiel S, Faure B, Kawato M, Ho SYW, Marshall B, Tsuchida S, Miyazaki JI, Fujiwara Y. Adaptive radiation of chemosymbiotic deep-sea mussels. Proc Biol Sci 2013; 280:20131243. [PMID: 24048154 PMCID: PMC3779325 DOI: 10.1098/rspb.2013.1243] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiations present fascinating opportunities for studying the evolutionary process. Most cases come from isolated lakes or islands, where unoccupied ecological space is filled through novel adaptations. Here, we describe an unusual example of an adaptive radiation: symbiotic mussels that colonized island-like chemosynthetic environments such as hydrothermal vents, cold seeps and sunken organic substrates on the vast deep-sea floor. Our time-calibrated molecular phylogeny suggests that the group originated and acquired sulfur-oxidizing symbionts in the Late Cretaceous, possibly while inhabiting organic substrates and long before its major radiation in the Middle Eocene to Early Oligocene. The first appearance of intracellular and methanotrophic symbionts was detected only after this major radiation. Thus, contrary to expectations, the major radiation may have not been triggered by the evolution of novel types of symbioses. We hypothesize that environmental factors, such as increased habitat availability and/or increased dispersal capabilities, sparked the radiation. Intracellular and methanotrophic symbionts were acquired in several independent lineages and marked the onset of a second wave of diversification at vents and seeps. Changes in habitat type resulted in adaptive trends in shell lengths (related to the availability of space and energy, and physiological trade-offs) and in the successive colonization of greater water depths.
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Affiliation(s)
- Julien Lorion
- Marine Ecosystems Research Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), , 2-15 Natsushima, Yokosuka 237-0061, Japan, Geoscience Center, Geobiology Group, University of Göttingen, , Goldschmidtstrasse 3, Göttingen 37077, Germany, Department of Biology, Pennsylvania State University, , University Park, PA 16802, USA, School of Biological Sciences, University of Sydney, , Sydney, New South Wales 2006, Australia, Museum of New Zealand Te Papa Tongarewa, , PO Box 467, 169 Tory St., Te Aro, Wellington 6011, New Zealand, Faculty of Education and Human Sciences, University of Yamanashi, , Kofu, Yamanashi 400-8510, Japan
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17
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Thubaut J, Corbari L, Gros O, Duperron S, Couloux A, Samadi S. Integrative biology of Idas iwaotakii (Habe, 1958), a 'model species' associated with sunken organic substrates. PLoS One 2013; 8:e69680. [PMID: 23894520 PMCID: PMC3722101 DOI: 10.1371/journal.pone.0069680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
The giant bathymodioline mussels from vents have been studied as models to understand the adaptation of organisms to deep-sea chemosynthetic environments. These mussels are closely related to minute mussels associated to organic remains decaying on the deep-sea floor. Whereas biological data accumulate for the giant mussels, the small mussels remain poorly studied. Despite this lack of data for species living on organic remains it has been hypothesized that during evolution, contrary to their relatives from vents or seeps, they did not acquire highly specialized biological features. We aim at testing this hypothesis by providing new biological data for species associated with organic falls. Within Bathymodiolinae a close phylogenetic relationship was revealed between the Bathymodiolus sensu stricto lineage (i.e. “thermophilus” lineage) which includes exclusively vent and seep species, and a diversified lineage of small mussels, attributed to the genus Idas, that includes mostly species from organic falls. We selected Idas iwaotakii (Habe, 1958) from this latter lineage to analyse population structure and to document biological features. Mitochondrial and nuclear markers reveal a north-south genetic structure at an oceanic scale in the Western Pacific but no structure was revealed at a regional scale or as correlated with the kind of substrate or depth. The morphology of larval shells suggests substantial dispersal abilities. Nutritional features were assessed by examining bacterial diversity coupled by a microscopic analysis of the digestive tract. Molecular data demonstrated the presence of sulphur-oxidizing bacteria resembling those identified in other Bathymodiolinae. In contrast with most Bathymodiolus s.s. species the digestive tract of I. iwaotakii is not reduced. Combining data from literature with the present data shows that most of the important biological features are shared between Bathymodiolus s.s. species and its sister-lineage. However Bathymodiolus s.s. species are ecologically more restricted and also display a lower species richness than Idas species.
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Affiliation(s)
- Justine Thubaut
- Département Systématique et Evolution, UMR 7138 UPMC-IRD-MNHN-CNRS, Muséum national d'Histoire naturelle, Paris, France.
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18
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Li J, Foighil DO, Park JK. Triton's trident: cryptic Neogene divergences in a marine clam (Lasaea australis) correspond to Australia's three temperate biogeographic provinces. Mol Ecol 2013; 22:1933-46. [PMID: 23379611 DOI: 10.1111/mec.12220] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/14/2012] [Accepted: 12/18/2012] [Indexed: 11/27/2022]
Abstract
The southern coast of Australia is composed of three distinct biogeographic provinces distinguished primarily by intertidal community composition. Several ecological mechanisms have been proposed to explain their formation and persistence, but no consensus has been reached. The marine clam Lasaea australis is arguably the most common bivalve on southern Australian rocky shores and occurs in all three provinces. Here, we tested if this species exhibits cryptic genetic structuring corresponding to the provinces and if so, what mechanisms potentially drove its divergence. Variation in two mitochondrial genes (16S and COIII) and one nuclear gene (ITS2) was assayed to test for genetic structuring and to reconstruct the clam's phylogenetic history. Our results showed that L. australis is comprised of three cryptic mitochondrial clades, each corresponding almost perfectly to one of the three biogeographic provinces. Divergence time estimates place their cladogenesis in the Neogene. The trident-like topology and Neogene time frame of L. australis cladogenesis are incongruent with Quaternary vicariance predictions: a two-clade topology produced by Pleistocene Bass Strait land bridge formation. We hypothesize that the interaction of the Middle Miocene Climate Transition with the specific geography of the southern coastline of Australia was the primary cladogenic driver in this clam lineage. Additional in-depth studies of the endemic southern Australian marine biota across all three provinces are needed to establish the generality of this proposed older framework for regional cladogenesis.
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Affiliation(s)
- Jingchun Li
- Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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19
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Johnson SB, Won YJ, Harvey JB, Vrijenhoek RC. A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents. BMC Evol Biol 2013; 13:21. [PMID: 23347448 PMCID: PMC3740784 DOI: 10.1186/1471-2148-13-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/11/2013] [Indexed: 11/24/2022] Open
Abstract
Background The inhabitants of deep-sea hydrothermal vents occupy ephemeral island-like habitats distributed sporadically along tectonic spreading-centers, back-arc basins, and volcanically active seamounts. The majority of vent taxa undergo a pelagic larval phase, and thus varying degrees of geographical subdivision, ranging from no impedance of dispersal to complete isolation, often exist among taxa that span common geomorphological boundaries. Two lineages of Bathymodiolus mussels segregate on either side of the Easter Microplate, a boundary that separates the East Pacific Rise from spreading centers connected to the Pacific-Antarctic Ridge. Results A recent sample from the northwest flank of the Easter Microplate contained an admixture of northern and southern mitochondrial haplotypes and corresponding alleles at five nuclear gene loci. Genotypic frequencies in this sample did not fit random mating expectation. Significant heterozygote deficiencies at nuclear loci and gametic disequilibria between loci suggested that this transitional region might be a ‘Tension Zone’ maintained by immigration of parental types and possibly hybrid unfitness. An analysis of recombination history in the nuclear genes suggests a prolonged history of parapatric contact between the two mussel lineages. We hereby elevate the southern lineage to species status as Bathymodiolus antarcticus n. sp. and restrict the use of Bathymodiolus thermophilus to the northern lineage. Conclusions Because B. thermophilus s.s. exhibits no evidence for subdivision or isolation-by-distance across its 4000 km range along the EPR axis and Galápagos Rift, partial isolation of B. antarcticus n. sp. requires explanation. The time needed to produce the observed degree of mitochondrial differentiation is consistent with the age of the Easter Microplate (2.5 to 5.3 million years). The complex geomorphology of the Easter Microplate region forces strong cross-axis currents that might disrupt self-recruitment of mussels by removing planktotrophic larvae from the ridge axis. Furthermore, frequent local extinction events in this tectonically dynamic region might produce a demographic sink rather than a source for dispersing mussel larvae. Historical changes in tectonic rates and current patterns appear to permit intermittent contact and introgression between the two species.
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Affiliation(s)
- Shannon B Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039-9644, USA.
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20
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Addamo AM, Reimer JD, Taviani M, Freiwald A, Machordom A. Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity. PLoS One 2012; 7:e50215. [PMID: 23209679 PMCID: PMC3509136 DOI: 10.1371/journal.pone.0050215] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 10/22/2012] [Indexed: 11/25/2022] Open
Abstract
The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.
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Affiliation(s)
- Anna M Addamo
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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21
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van der Heijden K, Petersen JM, Dubilier N, Borowski C. Genetic connectivity between north and south Mid-Atlantic Ridge chemosynthetic bivalves and their symbionts. PLoS One 2012; 7:e39994. [PMID: 22792208 PMCID: PMC3391212 DOI: 10.1371/journal.pone.0039994] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 06/04/2012] [Indexed: 11/18/2022] Open
Abstract
Transform faults are geological structures that interrupt the continuity of mid-ocean ridges and can act as dispersal barriers for hydrothermal vent organisms. In the equatorial Atlantic Ocean, it has been hypothesized that long transform faults impede gene flow between the northern and the southern Mid-Atlantic Ridge (MAR) and disconnect a northern from a southern biogeographic province. To test if there is a barrier effect in the equatorial Atlantic, we examined phylogenetic relationships of chemosynthetic bivalves and their bacterial symbionts from the recently discovered southern MAR hydrothermal vents at 5°S and 9°S. We examined Bathymodiolus spp. mussels and Abyssogena southwardae clams using the mitochondrial cytochrome c oxidase subunit I (COI) gene as a phylogenetic marker for the hosts and the bacterial 16S rRNA gene as a marker for the symbionts. Bathymodiolus spp. from the two southern sites were genetically divergent from the northern MAR species B. azoricus and B. puteoserpentis but all four host lineages form a monophyletic group indicating that they radiated after divergence from their northern Atlantic sister group, the B. boomerang species complex. This suggests dispersal of Bathymodiolus species from north to south across the equatorial belt. 16S rRNA genealogies of chemoautotrophic and methanotrophic symbionts of Bathymodiolus spp. were inconsistent and did not match the host COI genealogy indicating disconnected biogeography patterns. The vesicomyid clam Abyssogena southwardae from 5°S shared an identical COI haplotype with A. southwardae from the Logatchev vent field on the northern MAR and their symbionts shared identical 16S phylotypes, suggesting gene flow across the Equator. Our results indicate genetic connectivity between the northern and southern MAR and suggest that a strict dispersal barrier does not exist.
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Affiliation(s)
| | - Jillian M. Petersen
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Dubilier
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christian Borowski
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- * E-mail:
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22
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Teixeira S, Serrão EA, Arnaud-Haond S. Panmixia in a fragmented and unstable environment: the hydrothermal shrimp Rimicaris exoculata disperses extensively along the Mid-Atlantic Ridge. PLoS One 2012; 7:e38521. [PMID: 22679511 PMCID: PMC3367947 DOI: 10.1371/journal.pone.0038521] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 05/05/2012] [Indexed: 12/03/2022] Open
Abstract
Dispersal plays a fundamental role in the evolution and persistence of species, and especially for species inhabiting extreme, ephemeral and highly fragmented habitats as hydrothermal vents. The Mid-Atlantic Ridge endemic shrimp species Rimicaris exoculata was studied using microsatellite markers to infer connectivity along the 7100-Km range encompassing the sampled sites. Astonishingly, no genetic differentiation was found between individuals from the different geographic origins, supporting a scenario of widespread large-scale dispersal despite the habitat distance and fragmentation. We hypothesize that delayed metamorphosis associated to temperature differences or even active directed migration dependent on physical and/or chemical stimuli could explain these results and warrant further studies on adaptation and dispersal mechanisms.
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Affiliation(s)
- Sara Teixeira
- Ifremer - Centre de Brest, Departement Etude des Ecosystèmes Profonds - DEEP, Brest, France.
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23
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Duvaux L, Belkhir K, Boulesteix M, Boursot P. Isolation and gene flow: inferring the speciation history of European house mice. Mol Ecol 2011; 20:5248-64. [PMID: 22066696 DOI: 10.1111/j.1365-294x.2011.05343.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inferring the history of isolation and gene flow during species differentiation can inform us on the processes underlying their formation. Following their recent expansion in Europe, two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus) have formed a hybrid zone maintained by hybrid incompatibilities and possibly behavioural reinforcement, offering a good model of incipient speciation. We reconstruct the history of their divergence using an approximate Bayesian computation framework and sequence variation at 57 autosomal loci. We find support for a long isolation period preceding the advent of gene flow around 200,000 generations ago, much before the formation of the European hybrid zone a few thousand years ago. The duration of the allopatric episode appears long enough (74% of divergence time) to explain the accumulation of many post-zygotic incompatibilities expressed in the present hybrid zone. The ancient contact inferred could have played a role in mating behaviour divergence and laid the ground for further reinforcement. We suggest that both subspecies originally colonized the Middle East from the northern Indian subcontinent, domesticus settling on the shores of the Persian Gulf and musculus on those of the Caspian Sea. Range expansions during interglacials would have induced secondary contacts, presumably in Iran, where they must have also interacted with Mus musculus castaneus. Future studies should incorporate this possibility, and we point to Iran and its surroundings as a hot spot for house mouse diversity and speciation studies.
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Affiliation(s)
- Ludovic Duvaux
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, CC063, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
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24
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Miglietta MP, Faucci A, Santini F. Speciation in the sea: overview of the symposium and discussion of future directions. Integr Comp Biol 2011; 51:449-55. [PMID: 21593140 DOI: 10.1093/icb/icr024] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Speciation remains one of the most controversial and least understood topics in evolution. About 75% of the earth's surface is covered by oceans. However, most of what we currently know about speciation is strongly biased toward terrestrial and freshwater organisms. Here, we discuss some of the major advances of the past two decades in our understanding of speciation in the sea and outline promising future directions that were gathered during the 2011 SICB Symposium "Speciation in the Sea."
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Affiliation(s)
- Maria P Miglietta
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46566, USA.
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25
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Zheng XM, Ge S. Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara). Mol Ecol 2010; 19:2439-54. [PMID: 20653085 DOI: 10.1111/j.1365-294x.2010.04674.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ecological divergence plays a prominent role in the process of speciation, but how divergence occurs in the face of gene flow is still less clear, and remains controversial among evolutionists. Here we investigated the nucleotide diversity, divergence and gene flow between Oryza nivara and O. rufipogon using sequences of seven chloroplast and nuclear loci. By analysing samples from 26 wild populations across the geographic ranges of the two species, we showed that both species were highly structured and O. rufipogon maintained a higher level of species-wide diversity than O. nivara. Notably, phylogenetic, amova and FST analyses were unable to detect significant nucleotide differentiation between the two species. We estimated that the two species began to diverge at c. 0.16 million years ago. Our coalescent-based simulations strongly rejected the simple isolation model of zero migration between species, but rather provided unambiguous evidence of bidirectional gene flow between species, particularly from O. rufipogon to O. nivara. Our simulations also indicated that gene flow was recurrent during the divergence process rather than arising from secondary contact after allopatric divergence. In conjunction with different morphological and life-history traits and habitat preference in the two species, this study supports the hypothesis that these Oryza species are better treated as ecotypes that diverged quite recently and are still under the process of divergence. Importantly, we demonstrate the ecological divergence between O. rufipogon and O. nivara in the presence of significant gene flow, implying that natural selection plays a primary role in driving the divergence of the two Oryza species.
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Affiliation(s)
- Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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26
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VRIJENHOEK ROBERTC. Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations. Mol Ecol 2010; 19:4391-411. [DOI: 10.1111/j.1365-294x.2010.04789.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Plouviez S, Le Guen D, Lecompte O, Lallier FH, Jollivet D. Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana. BMC Evol Biol 2010; 10:220. [PMID: 20663123 PMCID: PMC2924869 DOI: 10.1186/1471-2148-10-220] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 07/22/2010] [Indexed: 11/20/2022] Open
Abstract
Background Comparative phylogeography recently performed on the mitochondrial cytochrome oxidase I (mtCOI) gene from seven deep-sea vent species suggested that the East Pacific Rise fauna has undergone a vicariant event with the emergence of a north/south physical barrier at the Equator 1-2 Mya. Within this specialised fauna, the tube-dwelling polychaete Alvinella pompejana showed reciprocal monophyly at mtCOI on each side of the Equator (9°50'N/7°25'S), suggesting potential, ongoing allopatric speciation. However, the development of a barrier to gene flow is a long and complex process. Secondary contact between previously isolated populations can occur when physical isolation has not persisted long enough to result in reproductive isolation between genetically divergent lineages, potentially leading to hybridisation and subsequent allelic introgression. The present study evaluates the strength of the equatorial barrier to gene flow and tests for potential secondary contact zones between A. pompejana populations by comparing the mtCOI gene with nuclear genes. Results Allozyme frequencies and the analysis of nucleotide polymorphisms at three nuclear loci confirmed the north/south genetic differentiation of Alvinella pompejana populations along the East Pacific Rise. Migration was oriented north-to-south with a moderate allelic introgression between the two geographic groups over a narrow geographic range just south of the barrier. Multilocus analysis also indicated that southern populations have undergone demographic expansion as previously suggested by a multispecies approach. A strong shift in allozyme frequencies together with a high level of divergence between alleles and a low number of 'hybrid' individuals were observed between the northern and southern groups using the phosphoglucomutase gene. In contrast, the S-adenosylhomocysteine hydrolase gene exhibited reduced diversity and a lack of population differentiation possibly due to a selective sweep or hitch-hiking. Conclusions The equatorial barrier leading to the separation of East Pacific Rise vent fauna into two distinct geographic groups is still permeable to migration, with a probable north-to-south migration route for A. pompejana. This separation also coincides with demographic expansion in the southern East Pacific Rise. Our results suggest that allopatry resulting from ridge offsetting is a common mechanism of speciation for deep-sea hydrothermal vent organisms.
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Affiliation(s)
- Sophie Plouviez
- Université Pierre et Marie Curie-Paris 6, Laboratoire Adaptation et Diversité en Milieu Marin, Roscoff, France
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Characterization of 18 polymorphic microsatellite loci from Bathymodiolus manusensis (Bivalvia, Mytilidae) from deep-sea hydrothermal vents. CONSERV GENET RESOUR 2010. [DOI: 10.1007/s12686-010-9272-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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New insights into diversity and evolution of deep-sea Mytilidae (Mollusca: Bivalvia). Mol Phylogenet Evol 2010; 57:71-83. [PMID: 20558305 DOI: 10.1016/j.ympev.2010.05.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 05/26/2010] [Accepted: 05/29/2010] [Indexed: 11/22/2022]
Abstract
Bathymodiolinae mussels have been used as a biological model to better understand the evolutionary origin of faunas associated with deep-sea hydrothermal vents and cold seeps. Most studies to date, however, have sampled with a strong bias towards vent and seep species, mainly because of a lack of knowledge of closely related species from organic falls. Here we reassess the species diversity of deep-sea mussels using two genes and a large taxon sample from the South-Western Pacific. This new taxonomic framework serves as a basis for a phylogenetic investigation of their evolutionary history. We first highlight an unexpected allopatric pattern and suggest that mussels usually reported from organic falls are in fact poorly specialized with regard to their environment. This challenges the adaptive scenarios proposed to explain the diversification of the group. Second, we confirm that deep-sea mussels arose from organic falls and then colonized hydrothermal vents and cold seeps in multiple events. Overall, this study constitutes a new basis for further phylogenetic investigations and a global systematic revision of deep-sea mussels.
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