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Morard R, Darling KF, Weiner AKM, Hassenrück C, Vanni C, Cordier T, Henry N, Greco M, Vollmar NM, Milivojevic T, Rahman SN, Siccha M, Meilland J, Jonkers L, Quillévéré F, Escarguel G, Douady CJ, de Garidel-Thoron T, de Vargas C, Kucera M. The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton. Biol Rev Camb Philos Soc 2024; 99:1218-1241. [PMID: 38351434 DOI: 10.1111/brv.13065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 07/06/2024]
Abstract
The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Kate F Darling
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3JW, UK
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Agnes K M Weiner
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, Bergen, 5007, Norway
| | - Christiane Hassenrück
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Seestrasse 15, Warnemünde, 18119, Germany
| | - Chiara Vanni
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Tristan Cordier
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, Bergen, 5007, Norway
| | - Nicolas Henry
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, Roscoff, 29680, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, 75016, France
| | - Mattia Greco
- Institut de Ciències del Mar, Passeig Marítim de la Barceloneta, Barcelona, 37-49, Spain
| | - Nele M Vollmar
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, Bergen, 5007, Norway
| | - Tamara Milivojevic
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shirin Nurshan Rahman
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Michael Siccha
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Julie Meilland
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Lukas Jonkers
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Frédéric Quillévéré
- Univ Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, UMR CNRS 5276 LGL-TPE, Villeurbanne, F-69622, France
| | - Gilles Escarguel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, F-69622, France
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, F-69622, France
- Institut Universitaire de France, Paris, France
| | | | - Colomban de Vargas
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, Roscoff, 29680, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR7144, Place Georges Teissier, Roscoff, 29680, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
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Kulagin DN, Lunina AA, Simakova UV, Vedenin AA, Vereshchaka AL. Revision of the 'Acanthephyra purpurea' species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic. Mol Phylogenet Evol 2024; 195:108070. [PMID: 38574781 DOI: 10.1016/j.ympev.2024.108070] [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: 12/28/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
We inventoried all nine species of the 'Acanthephyra purpurea' complex, one of the most abundant and cosmopolitan group of mesopelagic shrimps. We used 119 specimens at hand and genetic data for 124 specimens from GenBank and BOLD. Phylogenetic analysis of four genes (COI, 16S, NaK, and enolase) showed that the 'Acanthephyra purpurea' complex is polyphyletic and encompasses two species groups, 'A. purpurea' (mostly Atlantic) and 'A. smithi' (Indo-West Pacific). The 'A. purpurea' species group consists of two major molecular clades A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa. Molecular data suggest that hitherto accepted species A. acanthitelsonis, A. pelagica, and A. sica should be considered as synonyms. The Atlantic is inhabited by at least two cryptic genetic lineages of A. pelagica and A. quadrispinosa. Morphological analyses of qualitative and quantitative (900 measurements) characters resulted in a tabular key to species and in a finding of four evolutionary traits. Atlantic species showed various scenarios of diversification visible on mitochondrial gene level, nuclear gene level, and morphological level. We recorded and discussed similar phylogeographic trends in diversification and in distribution of genetic lineages within two different clades: A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa.
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Affiliation(s)
- Dmitry N Kulagin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Anastasiia A Lunina
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Ulyana V Simakova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | | | - Alexander L Vereshchaka
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia.
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3
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Diachroneity Rules the Mid-Latitudes: A Test Case Using Late Neogene Planktic Foraminifera across the Western Pacific. GEOSCIENCES 2022. [DOI: 10.3390/geosciences12050190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Planktic foraminifera are commonly used for first-order age control in deep-sea sediments from low-latitude regions based on a robust tropical–subtropical zonation scheme. Although multiple Neogene planktic foraminiferal biostratigraphic zonations for mid-latitude regions exist, quantification of diachroneity for the species used as datums to test paleobiogeographic patterns of origination and dispersal is lacking. Here, we update the age models for seven southwest-Pacific deep-sea sites using calcareous nannofossil and bolboform biostratigraphy and magnetostratigraphy, and use 11 sites between 37.9° N and 40.6° S in the western Pacific to correlate existing planktic foraminiferal biozonations and quantify the diachroneity of species used as datums. For the first time, northwest and southwest Pacific biozones are correlated and compared to the global tropical planktic foraminiferal biozonation. We find a high degree of diachroneity in the western Pacific, within and between the northwest and southwest regions, and between the western Pacific and the tropical zonation. Importantly, some datums that are found to be diachronous between regions have reduced diachroneity within regions. Much work remains to refine regional planktic foraminiferal biozonations and more fully understand diachroneity between the tropics and mid-latitudes. This study indicates that diachroneity is the rule for Late Neogene planktic foraminifera, rather than the exception, in mid-latitude regions.
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Thakur R, Collens A, Greco M, Sleith RS, Grattepanche JD, Katz LA. Newly designed foraminifera primers identify habitat-specific lineages through metabarcoding analyses. J Eukaryot Microbiol 2022; 69:e12913. [PMID: 35332619 DOI: 10.1111/jeu.12913] [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: 11/29/2022]
Abstract
Foraminifera include diverse shell-building lineages found in a wide array of aquatic habitats from the deep-sea to intertidal zones to brackish and freshwater ecosystems. Recent estimates of morphological and molecular foraminifera diversity have increased the knowledge of foraminiferal diversity, which is critical as these lineages are used as bioindicators of past and present environmental perturbation. However, a comparative analysis of foraminiferal biodiversity between their major habitats (freshwater, brackish, intertidal, and marine) is underexplored, particularly using molecular tools. Here, we present metabarcoding survey of foraminiferal diversity across different ecosystems using newly designed foraminifera-specific primers that target the hypervariable regions of the foraminifera SSU-rRNA gene (~250-300bp long). We tested these primer sets on four foraminifera species and then across several environments: the intertidal zone, coastal ecosystems, and freshwater vernal pools. We retrieved 655 operational taxonomic units (OTUs); the majority are undetermined taxa that have no closely-matching sequences in the database. Furthermore, we identified 163 OTUs with distinct habitat preferences. Most of the observed OTUs belonged to lineages of single-chambered foraminifera, including poorly explored freshwater foraminifera which encompass a clade of Reticulomyxa-like forms. Our pilot study provides the community with an additional set of newly designed and taxon-specific primers to elucidate foraminiferal diversity across different habitats.
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Affiliation(s)
- Rabindra Thakur
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Adena Collens
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA
| | - Mattia Greco
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,Temple University, Department of Biology, Philadelphia, Pennsylvania, USA
| | - Robin S Sleith
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA
| | - Jean-David Grattepanche
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Laura A Katz
- Smith College, Department of Biological Science, Northampton, Massachusetts, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
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Spatiotemporal Variations in Antarctic Protistan Communities Highlight Phytoplankton Diversity and Seasonal Dominance by a Novel Cryptophyte Lineage. mBio 2021; 12:e0297321. [PMID: 34903046 PMCID: PMC8669470 DOI: 10.1128/mbio.02973-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Andvord fjord in the West Antarctic Peninsula (WAP) is known for its productivity and abundant megafauna. Nevertheless, seasonal patterns of the molecular diversity and abundance of protistan community members underpinning WAP productivity remain poorly resolved. We performed spring and fall expeditions pursuing protistan diversity, abundance of photosynthetic taxa, and the connection to changing conditions. 18S rRNA amplicon sequence variant (ASV) profiles revealed diverse predatory protists spanning multiple eukaryotic supergroups, alongside enigmatic heterotrophs like the Picozoa. Among photosynthetic protists, cryptophyte contributions were notable. Analysis of plastid-derived 16S rRNA ASVs supported 18S ASV results, including a dichotomy between cryptophytes and diatom contributions previously reported in other Antarctic regions. We demonstrate that stramenopile and cryptophyte community structures have distinct attributes. Photosynthetic stramenopiles exhibit high diversity, with the polar diatom Fragilariopsis cylindrus, unidentified Chaetoceros species, and others being prominent. Conversely, ASV analyses followed by environmental full-length rRNA gene sequencing, electron microscopy, and flow cytometry revealed that a novel alga dominates the cryptophytes. Phylogenetic analyses established that TPG clade VII, as named here, is evolutionarily distinct from cultivated cryptophyte lineages. Additionally, cryptophyte cell abundance correlated with increased water temperature. Analyses of global data sets showed that clade VII dominates cryptophyte ASVs at Southern Ocean sites and appears to be endemic, whereas in the Arctic and elsewhere, Teleaulax amphioxeia and Plagioselmis prolonga dominate, although both were undetected in Antarctic waters. Collectively, our studies provide baseline data against which future change can be assessed, identify different diversification patterns between stramenopiles and cryptophytes, and highlight an evolutionarily distinct cryptophyte clade that thrives under conditions enhanced by warming.
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6
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Latitudinal Differentiation among Modern Planktonic Foraminiferal Populations of Central Mediterranean: Species–Specific Distribution Patterns and Size Variability. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9050551] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Studies of the spatial distribution and size of modern planktonic foraminifera are still lacking in the Mediterranean Sea. In this study, 17 core-top sediments collected from a north-south transect along the central Mediterranean have been analyzed for planktonic foraminiferal content, in terms of their distributional pattern and intraspecific size variability. Among the analyzed planktonic foraminiferal species, Globigerina bulloides and Globigerinoides ruber (w) were the most abundant, presenting an antagonistic behavior and an overall decreasing trend in their average size values from Adriatic to Ionian sub-basins. Intraspecific differences have been also documented for G. ruber (w), with the dominant sensu stricto morphotype to present generally higher frequencies and more constant shell sizes than sensu lato. The greater size variability of the latter is possibly related to its adaptation in particular hydrographic conditions based on its depth habitat preference and ecological characteristics to reach the (sub)optimum growth conditions. The rest of the species occur in minor percentages and show on average 11% increase with decreasing latitude characterized by distinct species-specific size variations along the transect. Our results show that the relationship between planktonic foraminifera shell size and abundance or sea surface temperature are either absent or weaker than previously reported for other regions and that in central Mediterranean assemblages’ size may be mainly related to nutrient availability. Besides the environmental parameters (sea surface temperature, primary productivity, water depth, stratification), the possible hidden cryptic diversity, still lingers to be consistently determined, could give a better understanding of the geographic and morphological differentiation within the Mediterranean planktonic populations.
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7
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Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula. Sci Rep 2021; 11:1368. [PMID: 33446791 PMCID: PMC7809266 DOI: 10.1038/s41598-020-80568-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023] Open
Abstract
Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris, which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.
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8
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Janik P, Lado C, Ronikier A. Range-wide Phylogeography of a Nivicolous Protist Didymium nivicola Meyl. (Myxomycetes, Amoebozoa): Striking Contrasts Between the Northern and the Southern Hemisphere. Protist 2020; 171:125771. [PMID: 33171353 DOI: 10.1016/j.protis.2020.125771] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/23/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022]
Abstract
Soil protists play a crucial role in terrestrial ecosystems and often show immense taxonomic diversity. However, for many groups, distribution patterns remain largely unknown. We investigated range-wide intraspecific diversity of a specialized airborne protist (Didymium nivicola Meyl.) that occupies a narrow ecological niche associated with long-lasting snow cover. We sampled 122 collections covering all areas where the species was recorded worldwide. We obtained 105 and 41 sequences of small ribosomal subunit rDNA (SSU) and elongation factor 1-alpha (EF1A), respectively. While the species is very diverse in the austral Andes, Southern Hemisphere (SH; 17 SSU ribotypes and 12 EF1A genotypes identified), its populations are genetically uniform across three continents of the Northern Hemisphere (NH; single ribotype, single genotype). Our results indicate the austral Andes as a possible diversification centre for D. nivicola where populations seem to reproduce sexually. Two main parts of the range display highly contrasting genetic patterns, thus biogeographical history and dynamics. Current distribution of D. nivicola in the NH is likely a result of a dispersal event from the SH and subsequent long-distance dispersal (LDD) that might be associated with a shift to asexual mode of reproduction.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland.
| | - Carlos Lado
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
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9
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Jossart Q, Kochzius M, Danis B, Saucède T, Moreau CVE. Diversity of the Pterasteridae (Asteroidea) in the Southern Ocean: a molecular and morphological approach. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
An integrative approach is crucial in discrimination of species, especially for taxa that are difficult to identify based on morphological characters. In this study, we combine genetics and morphology to assess the diversity of Pterasteridae, a sea star family diversified in deep-sea and polar environments. Because of their derived anatomy and the frequent loss of characters during preservation, Pterasteridae are a suitable case for an integrative study. The molecular identification of 191 specimens (mostly from the Southern Ocean) suggests 26–33 species in three genera (Diplopteraster, Hymenaster and Pteraster), which match the morphological identification in 54–62% of cases. The mismatches are either different molecular units that are morphologically indistinguishable (e.g. Pteraster stellifer units 2 and 4) or, conversely, nominal species that are genetically identical (e.g. Hymenaster coccinatus/densus/praecoquis). Several species are shared between the Northern and Southern Hemispheres (e.g. Pteraster jordani/affinis). In conclusion, the taxonomic status of some groups is confirmed, but for others we find the need to re-evaluate the taxonomy at both genus and species levels. This work significantly increases the DNA barcode library of the Southern Ocean species and merges taxonomic information into an identification key that could become a baseline for future studies (pterasteridae-so.identificationkey.org).
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Affiliation(s)
- Quentin Jossart
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Bruno Danis
- Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Thomas Saucède
- Biogéosciences, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Camille V E Moreau
- Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Biogéosciences, Université Bourgogne Franche Comté (UBFC), Dijon, France
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10
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Pawłowska J, Wollenburg JE, Zajączkowski M, Pawlowski J. Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA. Sci Rep 2020; 10:15102. [PMID: 32934321 PMCID: PMC7492196 DOI: 10.1038/s41598-020-72146-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.
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Affiliation(s)
- Joanna Pawłowska
- Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | | | | | - Jan Pawlowski
- Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.,University of Geneva, Geneva, Switzerland
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11
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Melo DCM, Lira SMA, Moreira APB, Freitas L, Lima CAD, Thompson F, Bertrand A, Silva AC, Neumann-Leitão S. Genetic diversity and connectivity of Flaccisagitta enflata (Chaetognatha: Sagittidae) in the tropical Atlantic ocean (northeastern Brazil). PLoS One 2020; 15:e0231574. [PMID: 32374742 PMCID: PMC7202658 DOI: 10.1371/journal.pone.0231574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/26/2020] [Indexed: 11/18/2022] Open
Abstract
The phylogeography of the holoplanktonic chaetognath Flaccisagitta enflata was investigated in the Tropical Western Atlantic (TWA). Considering the cosmopolitan range of this species and the fact that its entire life cycle is planktonic, the central hypothesis of this study is that F. enflata exhibits connectivity due to its high dispersal capacity, forming a panmictic population among the study sites. The evaluated areas included neritic (Port of Recife–PR, and Tamandaré - TA) and oceanic (Fernando de Noronha Archipelago—FN, Rocas Atoll—RA, Guará seamount—GS and Saint Peter and Saint Paul’s Archipelago—SPSPA) locations of the Brazilian Blue Amazon. We used COI gene sequences as molecular marker. Partial sequences (425 bp) were obtained for 116 specimens and employed to reconstruct the phylogeny, build an haplotype network, evaluate gene flow through a migration model, and estimate diversity indices, population structuring and demographic history. High levels of haplotype diversity (mean: 0.98) and moderate to high levels of nucleotide diversity (mean: 0.023) were observed. The phylogeny and the haplotype network topologies showed some geographic clustering, indicating local structuring in GS and PR. This finding was supported by the AMOVA high global Φst (0.033, significant) and some pairwise Φst comparisons (7 out of 15 were significantly >0). Significant differences suggested lower levels of connectivity when GS population was compared to those of FN and SPSPA; as well as when TA was compared to FN. These results might be related to particularities of the oceanic dynamics which rules the TWA, sustaining such dissimilarities. Structuring was also observed between PR and all oceanic locations. We hypothesize that the topography of the port inlet, enclosured by a reef barrier, may constrain the water turnover ratio and thus migration rates of F. enflata in the TWA. Accordingly, Migrate-N yielded a four metapopulations model (PR ⇌ TA ⇌ SPSPA+FN ⇌ GS+RA) as the best (highest probability; ~0.90) to represent the structuring of F. enflata in the TWA. Therefore, the null hypothesis of one randomly mating population cannot be accepted. The demographic evaluation demonstrated that the neutral hypothesis of stable populations may not be rejected for most of the locations. This work is the start point to broaden the knowledge on the phylogeography and population genetic structure of a numerically dominant species in the Western Atlantic, with key role in the marine trophic web.
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Affiliation(s)
- Danielle C. M. Melo
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
- * E-mail:
| | - Simone M. A. Lira
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
- Programa de pós-graduação em Ecologia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Ana Paula B. Moreira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas Freitas
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Camilla A. D. Lima
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- SAGE—COPPE, Centro de Gestão Tecnológica—CT2, Rio de Janeiro, Brazil
| | - Arnaud Bertrand
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
- Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, Recife, Brazil
- MARBEC, CNRS, Ifremer, IRD, Institut de Recherche pour le Développement (IRD), Université Montpellier, Sète, France
| | - Alex C. Silva
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, Brazil
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12
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Morard R, Füllberg A, Brummer GJA, Greco M, Jonkers L, Wizemann A, Weiner AKM, Darling K, Siccha M, Ledevin R, Kitazato H, de Garidel-Thoron T, de Vargas C, Kucera M. Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides. PLoS One 2019; 14:e0225246. [PMID: 31805130 PMCID: PMC6894840 DOI: 10.1371/journal.pone.0225246] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/31/2019] [Indexed: 11/19/2022] Open
Abstract
The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber "white" and G. ruber "pink", respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Angelina Füllberg
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Geert-Jan A. Brummer
- NIOZ Royal Netherlands Institute for Sea Research, Department of Ocean Systems, and Utrecht University, Den Burg, and Utrecht University, The Netherlands
- Vrije Universiteit Amsterdam, Department of Earth Sciences, Faculty of Science, Amsterdam, The Netherlands
| | - Mattia Greco
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Lukas Jonkers
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - André Wizemann
- Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Agnes K. M. Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Kate Darling
- School of GeoSciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- School of Geography and Sustainable Development, University of St Andrews, St Andrews, Scotland, United Kingdom
| | - Michael Siccha
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Ronan Ledevin
- UMR5199 PACEA, Université de Bordeaux, Allée Geoffroy Saint Hilaire, Pessac, France
| | - Hiroshi Kitazato
- Japan Agency for Marine Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
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13
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Bartels PJ, Fontaneto D, Roszkowska M, Nelson DR, Kaczmarek Ł. Latitudinal gradients in body size in marine tardigrades. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
Homeotherms and many poikilotherms display a positive relationship between body size and latitude, but this has rarely been investigated in microscopic animals. We analysed all published records of marine Tardigrada to address whether microscopic marine invertebrates have similar ecogeographical patterns to macroscopic animals. The data were analysed using spatially explicit generalized least squares models and linear models. We looked for latitudinal patterns in body size and species richness, testing for sampling bias and phylogenetic constraints. No latitudinal pattern was detected for species richness, and sampling bias was the strongest correlate of species richness. A hump-shaped increase in median body size with latitude was found, and the effect remained significant for the Northern Hemisphere but not for the Southern. The most significant effect supporting the latitudinal gradient was on minimum body size, with smaller species disappearing at higher latitudes. Our results suggest that biogeographical signals were observed for body size, albeit difficult to detect in poorly studied groups because of swamping from biased sampling effort and from low sample size. We did not find a significant correlation with the latitudinal pattern of body size and ecologically relevant net primary productivity.
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Affiliation(s)
- Paul J Bartels
- Department of Biology, Warren Wilson College, Asheville, NC, USA
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche, di Ricerca Sulle Acque CNR-IRSA, Verbania Pallanza, Italy
| | - Milena Roszkowska
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Poznan, Poznań, Poland
- Department of Bioenergetics, Adam Mickiewicz University, Poznan, Poznań, Poland
| | - Diane R Nelson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Poznan, Poznań, Poland
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14
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Vogt JC, Abed RMM, Albach DC, Palinska KA. Latitudinal gradient of cyanobacterial diversity in tidal flats. PLoS One 2019; 14:e0224444. [PMID: 31721816 PMCID: PMC6853291 DOI: 10.1371/journal.pone.0224444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 10/14/2019] [Indexed: 11/18/2022] Open
Abstract
Latitudinal diversity gradients are well-known for plants and animals, but only recently similar patterns have been described for some specific microbial communities in distinct habitats. Although microbial diversity is well-investigated worldwide, most of the studies are spatially too restricted to allow general statements about global diversity patterns. Additionally, methodological differences make it hard and often impossible to compare several studies. This study investigated the cyanobacterial diversity in tidal flats along geographical and ecological gradients based on high-throughput sequencing of 16S rRNA gene fragments (Illumina MiSeq) and environmental data on a large spatial scale from the subtropics to the Arctic. Latitude and strongly correlated environmental parameters (e.g. temperature) were identified as important drivers of cyanobacterial diversity on global scale resulting in a latitudinal diversity gradient similar to that known from plants and animals. Other non-correlated parameters (e.g. grain size) were shown to be more important on local scales, although no consistent pattern occurred across different locations. Among a total number of 989 operational taxonomic units (OTUs) only one cosmopolitan (classified as Coleofasciculus chthonoplastes), but many location-specific and putative endemic ones (78%) were detected. High proportions of rare members of the community (up to 86%) were found in all samples. Phylogenetic beta diversity was shown to be influenced by the developmental stage of the mat community becoming increasingly similar with increasing stabilization.
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Affiliation(s)
- Janina C Vogt
- Institute for Biology and Environmental Science (IBU), Biodiversity and Evolution of Plants, Carl-von-Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, Al Khoud, Muscat, Sultanate of Oman
| | - Dirk C Albach
- Institute for Biology and Environmental Science (IBU), Biodiversity and Evolution of Plants, Carl-von-Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Katarzyna A Palinska
- Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, al. Marszałka Józefa Piłsudskiego 46, Gdynia, Poland
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15
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Moreau C, Danis B, Jossart Q, Eléaume M, Sands C, Achaz G, Agüera A, Saucède T. Is reproductive strategy a key factor in understanding the evolutionary history of Southern Ocean Asteroidea (Echinodermata)? Ecol Evol 2019; 9:8465-8478. [PMID: 31410254 PMCID: PMC6686340 DOI: 10.1002/ece3.5280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/04/2019] [Indexed: 12/12/2022] Open
Abstract
Life traits such as reproductive strategy can be determining factors of species evolutionary history and explain the resulting diversity patterns. This can be investigated using phylogeographic analyses of genetic units. In this work, the genetic structure of five asteroid genera with contrasting reproductive strategies (brooding: Diplasterias, Notasterias and Lysasterias versus broadcasting: Psilaster and Bathybiaster) was investigated in the Southern Ocean. Over 1,400 mtDNA cytochrome C oxidase subunit I (COI) sequences were analysed using five species delineation methods (ABGD, ASAP, mPTP, sGMYC and mGMYC), two phylogenetic reconstructions (ML and BA), and molecular clock calibrations, in order to examine the weight of reproductive strategy in the observed differences among phylogeographic patterns. We hypothesised that brooding species would show higher levels of genetic diversity and species richness along with a clearer geographic structuring than broadcasting species. In contrast, genetic diversity and species richness were not found to be significantly different between brooders and broadcasters, but broadcasters are less spatially structured than brooders supporting our initial hypothesis and suggesting more complex evolutionary histories associated to this reproductive strategy. Broadcasters' phylogeography can be explained by different scenarios including deep-sea colonisation routes, bipolarity or cosmopolitanism, and sub-Antarctic emergence for the genus Bathybiaster; Antarctic- New Zealand faunal exchanges across the Polar Front for the genus Psilaster. Brooders' phylogeography could support the previously formulated hypothesis of a past trans-Antarctic seaway established between the Ross and the Weddell seas during the Plio-Pleistocene. Our results also show, for the first time, that the Weddell Sea is populated by a mixed asteroid fauna originating from both the East and West Antarctic.
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Affiliation(s)
- Camille Moreau
- Marine Biology LabUniversité Libre de Bruxelles (ULB)Belgium
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐ComtéDijonFrance
| | - Bruno Danis
- Marine Biology LabUniversité Libre de Bruxelles (ULB)Belgium
| | - Quentin Jossart
- Marine Biology LabUniversité Libre de Bruxelles (ULB)Belgium
- Marine BiologyVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Marc Eléaume
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne UniversitéParisFrance
| | - Chester Sands
- Natural Environment Research CouncilBritish Antarctic SurveyCambridgeUK
| | - Guillaume Achaz
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne UniversitéParisFrance
- Centre Interdisciplinaire de Recherche en Biologie (CIRB), CNRSINSERM, Collège de FranceParisFrance
| | - Antonio Agüera
- Marine Biology LabUniversité Libre de Bruxelles (ULB)Belgium
| | - Thomas Saucède
- Biogéosciences, UMR 6282 CNRSUniversité Bourgogne Franche‐ComtéDijonFrance
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16
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Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K. Delineating closely related dinoflagellate lineages using phylotranscriptomics. JOURNAL OF PHYCOLOGY 2018; 54:571-576. [PMID: 29676790 DOI: 10.1111/jpy.12748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Recently radiated dinoflagellates Apocalathium aciculiferum (collected in Lake Erken, Sweden), Apocalathium malmogiense (Baltic Sea) and Apocalathium aff. malmogiense (Highway Lake, Antarctica) represent a lineage with an unresolved phylogeny. We determined their phylogenetic relationships using phylotranscriptomics based on 792 amino acid sequences. Our results showed that A. aciculiferum diverged from the other two closely related lineages, consistent with their different morphologies in cell size, relative cell length and presence of spines. We hypothesized that A. aff. malmogiense and A. malmogiense, which inhabit different hemispheres, are evolutionarily more closely related because they diverged from a marine common ancestor, adapting to a wide salinity range, while A. aciculiferum colonized a freshwater habitat, by acquiring adaptations to this environment, in particular, salinity intolerance. We show that phylotranscriptomics can resolve the phylogeny of recently diverged protists. This has broad relevance, given that many phytoplankton species are morphologically very similar, and single genes sometimes lack the information to determine species' relationships.
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Affiliation(s)
- Nataliia V Annenkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033, Irkutsk, Russia
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
- Bioinformatics Infrastructures for Life Sciences (BILS), Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Science (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim de la Barceloneta 37-49, E08003, Barcelona, Spain
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute, Erik Palmenin aukio 1, 00560, Helsinki, Finland
| | - Karin Rengefors
- Aquatic Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
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17
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Darling JA, Carlton JT. A Framework for Understanding Marine Cosmopolitanism in the Anthropocene. FRONTIERS IN MARINE SCIENCE 2018; 5:293. [PMID: 31019910 PMCID: PMC6475922 DOI: 10.3389/fmars.2018.00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recent years have witnessed growing appreciation for the ways in which human-mediated species introductions have reshaped marine biogeography. Despite this we have yet to grapple fully with the scale and impact of anthropogenic dispersal in both creating and determining contemporary distributions of marine taxa. In particular, the past several decades of research on marine biological invasions have revealed that broad geographic distributions of coastal marine organisms-historically referred to simply as "cosmopolitanism"-may belie complex interplay of both natural and anthropogenic processes. Here we describe a framework for understanding contemporary cosmopolitanism, informed by a synthesis of the marine bioinvasion literature. Our framework defines several novel categories in an attempt to provide a unified terminology for discussing cosmopolitan distributions in the world's oceans. We reserve the term eucosmopolitan to refer to those species for which data exist to support a true, natural, and prehistorically global (or extremely broad) distribution. While in the past this has been the default assumption for species observed to exhibit contemporary cosmopolitan distributions, we argue that given recent advances in marine invasion science this assignment should require positive evidence. In contrast, neocosmopolitan describes those species that have demonstrably achieved extensive geographic ranges only through historical anthropogenic dispersal, often facilitated over centuries of human maritime traffic. We discuss the history and human geography underpinning these neocosmopolitan distributions, and illustrate the extent to which these factors may have altered natural biogeographic patterns. We define the category pseudocosmopolitan to encompass taxa for which a broad distribution is determined (typically after molecular investigation) to reflect multiple, sometimes regionally endemic, lineages with uncertain taxonomic status; such species may remain cosmopolitan only so long as taxonomic uncertainty persists, after which they may splinter into multiple geographically restricted species. We discuss the methods employed to identify such species and to resolve both their taxonomic status and their biogeographic histories. We argue that recognizing these different types of cosmopolitanism, and the important role that invasion science has played in understanding them, is critically important for the future study of both historical and modern marine biogeography, ecology, and biodiversity.
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Affiliation(s)
- John A. Darling
- United States Environmental Protection Agency, National Exposure Research Laboratory, Research Triangle Park, NC, United States
| | - James T. Carlton
- Maritime Studies Program, Williams College-Mystic Seaport, Mystic, CT, United States
- Department of Biology, Williams College, Williamstown, MA, United States
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18
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Luo Z, Yang W, Leaw CP, Pospelova V, Bilien G, Liow GR, Lim PT, Gu H. Cryptic diversity within the harmful dinoflagellate Akashiwo sanguinea in coastal Chinese waters is related to differentiated ecological niches. HARMFUL ALGAE 2017; 66:88-96. [PMID: 28602257 DOI: 10.1016/j.hal.2017.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/16/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
Blooms of the harmful dinoflagellate Akashiwo sanguinea are responsible for the mass mortality of fish and invertebrates in coastal waters. This cosmopolitan species includes several genetically differentiated clades. Four clonal cultures were established by isolating single cells from Xiamen Harbour (the East China Sea) for morphological and genetic analyses. The cultures displayed identical morphology but were genetically different, thus revealing presence of cryptic diversity in the study area. New details of the apical structure complex of Akashiwo sanguinea were also found. To investigate whether the observed cryptic diversity was related to environmental differentiation, 634 cells were obtained from seasonal water samples collected from 2008 to 2012. These cells were sequenced by single-cell PCR. For comparison with Chinese material, additional large subunit ribosomal DNA sequences were obtained for three established strains from Malaysian and French waters. To examine potential ecological differentiation of the distinct genotypes, growth responses of the studied strains were tested under laboratory conditions at temperatures of 12°C to 33°C. These experiments showed four distinct ribotypes of A. sanguinea globally, with the ribotypes A and B co-occuring in Xiamen Harbour. Ribotype A of A. sanguinea was present year-round in Xiamen Harbour, but it only bloomed in the winter and spring, thus corresponding to the winter type. In contrast, A. sanguinea ribotype B bloomed only in the summer, corresponding to the summer type. This differentiation supports the temperature optimum conditions that were established for these two ribotypes in the laboratory. Ribotype A grew better at lower temperatures compared to ribotype B which preferred higher temperatures. These findings support the idea that various ribotypes of A. sanguinea correspond to distinct ecotypes and allopatric speciation occurred in different climatic regions followed by dispersal.
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Affiliation(s)
- Zhaohe Luo
- Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Weidong Yang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Vera Pospelova
- School of Earth and Ocean Sciences, University of Victoria, OEASB A405, P. O. Box 1700 16 STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Gwenael Bilien
- Ifremer, LER BO, Station de Biologie Marine, Place de la Croix, BP40537, F-29185 Concarneau Cedex, France
| | - Guat Ru Liow
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Haifeng Gu
- Third Institute of Oceanography, SOA, Xiamen, 361005, China.
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19
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Fenton IS, Pearson PN, Dunkley Jones T, Farnsworth A, Lunt DJ, Markwick P, Purvis A. The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150224. [PMID: 26977064 PMCID: PMC4810817 DOI: 10.1098/rstb.2015.0224] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Cenozoic planktonic foraminifera (PF) (calcareous zooplankton) have arguably the most detailed fossil record of any group. The quality of this record allows models of environmental controls on macroecology, developed for Recent assemblages, to be tested on intervals with profoundly different climatic conditions. These analyses shed light on the role of long-term global cooling in establishing the modern latitudinal diversity gradient (LDG)--one of the most powerful generalizations in biogeography and macroecology. Here, we test the transferability of environment-diversity models developed for modern PF assemblages to the Eocene epoch (approx. 56-34 Ma), a time of pronounced global warmth. Environmental variables from global climate models are combined with Recent environment-diversity models to predict Eocene richness gradients, which are then compared with observed patterns. The results indicate the modern LDG--lower richness towards the poles--developed through the Eocene. Three possible causes are suggested for the mismatch between statistical model predictions and data in the Early Eocene: the environmental estimates are inaccurate, the statistical model misses a relevant variable, or the intercorrelations among facets of diversity--e.g. richness, evenness, functional diversity--have changed over geological time. By the Late Eocene, environment-diversity relationships were much more similar to those found today.
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Affiliation(s)
- Isabel S Fenton
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Paul N Pearson
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Tom Dunkley Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alexander Farnsworth
- School of Geographical Sciences and Cabot Institute, University of Bristol, Bristol BS8 1SS, UK
| | - Daniel J Lunt
- School of Geographical Sciences and Cabot Institute, University of Bristol, Bristol BS8 1SS, UK
| | - Paul Markwick
- Getech Group plc. Elmete Hall, Elmete Lane, Leeds LS8 2LJ, UK
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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20
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Boltovskoy D, Correa N. Planktonic equatorial diversity troughs: fact or artifact? Latitudinal diversity gradients in Radiolaria. Ecology 2016; 98:112-124. [PMID: 27935028 DOI: 10.1002/ecy.1623] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/16/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
In contrast to the classical notion of an increasing biodiversity from the poles to the equator, a number of studies concluded that the diversity of marine species is highest at the middle latitudes, and decreases at the equator. Using a worldwide database critically compiled from 72 surveys (307 species, 4,807 water column and surface sediment samples), we analyzed the latitudinal gradients in species richness (LGSR) of a highly diversified group of marine holoplanktonic protists, the polycystine Radiolaria. Species richness values were corrected for uneven sample coverage and sample size, and contrasted with gradients in 11 environmental variables. Radiolarian species richness decreases from the equator to the poles both in the water column and in the surface sediments and is tightly coupled with temperature throughout the entire thermal range of marine waters. In the tropical Pacific Ocean, a conspicuous east-west gradient in diversity is also associated with temperature. Globally, diversity is negatively correlated with mean annual concentrations of nutrients (N, P, Si) and chlorophyll a. Disagreements with results reported for many other oceanic plankton may stem from the reduction of 3D distributional patterns onto 2D or 1D spaces, to the intermittent mixing of Subtropical and Subpolar species at the middle latitudes, and to a Mid-Domain Effect. The fact that radiolarian LGSR do not show this drop at the equator is partly due to methodological and database-related differences, and probably also in part a reflection of taxon-specific traits.
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Affiliation(s)
- Demetrio Boltovskoy
- Facultad de Ciencias Exactas y Naturales, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, 1428, Buenos Aires, Argentina
| | - Nancy Correa
- Servicio de Hidrografía Naval (Ministerio de Defensa) and Escuela de Ciencias del Mar (Instituto Universitario Naval), Av. Montes de Oca 2124, 1271, Buenos Aires, Argentina
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21
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Genetic Variations of the Parasitic Dinoflagellate Hematodinium Infecting Cultured Marine Crustaceans in China. Protist 2016; 167:597-609. [DOI: 10.1016/j.protis.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/09/2016] [Accepted: 10/08/2016] [Indexed: 12/24/2022]
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22
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Fenton IS, Pearson PN, Dunkley Jones T, Purvis A. Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments. PLoS One 2016; 11:e0165522. [PMID: 27851751 PMCID: PMC5112986 DOI: 10.1371/journal.pone.0165522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/13/2016] [Indexed: 11/18/2022] Open
Abstract
Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world's oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson's evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert.
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Affiliation(s)
- Isabel S. Fenton
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom
| | - Paul N. Pearson
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Tom Dunkley Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom
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Trovant B, Basso NG, Orensanz JM, Lessa EP, Dincao F, Ruzzante DE. Scorched mussels (Brachidontes spp., Bivalvia: Mytilidae) from the tropical and warm-temperate southwestern Atlantic: the role of the Amazon River in their speciation. Ecol Evol 2016; 6:1778-98. [PMID: 26929816 PMCID: PMC4758806 DOI: 10.1002/ece3.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Antitropicality is a distribution pattern where closely related taxa are separated by an intertropical latitudinal gap. Two potential examples include Brachidontes darwinianus (south eastern Brazil to Uruguay), considered by some authors as a synonym of B. exustus (Gulf of Mexico and the Caribbean), and B. solisianus, distributed along the Brazilian coast with dubious records north of the intertropical zone. Using two nuclear (18S and 28S rDNA) and one mitochondrial gene (mtDNA COI), we aimed to elucidate the phylogeographic and phylogenetic relationships among the scorched mussels present in the warm-temperate region of the southwest Atlantic. We evaluated a divergence process mediated by the tropical zone over alternative phylogeographic hypotheses. Brachidontes solisianus was closely related to B. exustus I, a species with which it exhibits an antitropical distribution. Their divergence time was approximately 2.6 Ma, consistent with the intensification of Amazon River flow. Brachidontes darwinianus, an estuarine species is shown here not to be related to this B. exustus complex. We suspect ancestral forms may have dispersed from the Caribbean to the Atlantic coast via the Trans-Amazonian seaway (Miocene). The third species, B rodriguezii is presumed to have a long history in the region with related fossil forms going back to the Miocene. Although scorched mussels are very similar in appearance, their evolutionary histories are very different, involving major historical contingencies as the formation of the Amazon River, the Panama Isthmus, and the last marine transgression.
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Affiliation(s)
- Berenice Trovant
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Néstor G. Basso
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - José María Orensanz
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Enrique P. Lessa
- Departamento de Ecología y EvoluciónFacultad de CienciasUniversidad de la RepúblicaIguá 4225C.P. 11400MontevideoUruguay
| | - Fernando Dincao
- Universidade Federal do Rio Grande – FURGAv. Itália km 8 Bairro Carreiros96203‐900Rio GrandeBrazil
| | - Daniel E. Ruzzante
- Department of BiologyDalhousie University1355 Oxford St.HalifaxNova ScotiaB3H 4R2Canada
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Ryšánek D, Elster J, Kováčik L, Škaloud P. Diversity and dispersal capacities of a terrestrial algal genusKlebsormidium(Streptophyta) in polar regions. FEMS Microbiol Ecol 2016; 92:fnw039. [DOI: 10.1093/femsec/fiw039] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 11/13/2022] Open
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25
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Nagai S, Hida K, Urusizaki S, Takano Y, Hongo Y, Kameda T, Abe K. Massively parallel sequencing-based survey of eukaryotic community structures in Hiroshima Bay and Ishigaki Island. Gene 2016; 576:681-9. [DOI: 10.1016/j.gene.2015.10.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Tyml T, Kostka M, Ditrich O, Dyková I. Vermistella arctica n. sp. Nominates the Genus Vermistella as a Candidate for Taxon with Bipolar Distribution. J Eukaryot Microbiol 2015; 63:210-9. [PMID: 26384711 DOI: 10.1111/jeu.12270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 08/28/2015] [Accepted: 08/29/2015] [Indexed: 11/26/2022]
Abstract
A new amoebozoan species, Vermistella arctica n. sp., is described from marine habitats in the central part of Svalbard archipelago. This is the first report on Arctic amoebae belonging to the genus Vermistella Moran and Anderson, 2007, the type species of which was described from the opposite pole of the planet. Psychrophily proved in the new strains qualifies the genus Vermistella as a bipolar taxon. Molecular phylogenetic analyses based on 18S rDNA and actin sequences did not show any affinity of the genus Vermistella to Stygamoeba regulata ATCC(®) 50892(™) strain. A close phylogenetic relationship was found between Vermistella spp. and a sequence originating from an environmental sample from Cariaco basin, the largest marine permanently anoxic system in the world. Possible mechanisms of bipolar distribution are discussed.
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Affiliation(s)
- Tomáš Tyml
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Institute of Parasitology, Biology Centre ASCR, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Martin Kostka
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Institute of Parasitology, Biology Centre ASCR, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Oleg Ditrich
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Iva Dyková
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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Yang H, Dai Y, Xu M, Zhang Q, Bian X, Tang J, Chen X. Metadata-mining of 18S rDNA sequences reveals that “everything is not everywhere” for glomeromycotan fungi. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1116-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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28
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Spezzaferri S, Kucera M, Pearson PN, Wade BS, Rappo S, Poole CR, Morard R, Stalder C. Fossil and genetic evidence for the polyphyletic nature of the planktonic foraminifera "Globigerinoides", and description of the new genus Trilobatus. PLoS One 2015; 10:e0128108. [PMID: 26020968 PMCID: PMC4447400 DOI: 10.1371/journal.pone.0128108] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/23/2015] [Indexed: 12/02/2022] Open
Abstract
Planktonic foraminifera are one of the most abundant and diverse protists in the oceans. Their utility as paleo proxies requires rigorous taxonomy and comparison with living and genetically related counterparts. We merge genetic and fossil evidence of "Globigerinoides", characterized by supplementary apertures on spiral side, in a new approach to trace their "total evidence phylogeny" since their first appearance in the latest Paleogene. Combined fossil and molecular genetic data indicate that this genus, as traditionally understood, is polyphyletic. Both datasets indicate the existence of two distinct lineages that evolved independently. One group includes "Globigerinoides" trilobus and its descendants, the extant "Globigerinoides" sacculifer, Orbulina universa and Sphaeroidinella dehiscens. The second group includes the Globigerinoides ruber clade with the extant G. conglobatus and G. elongatus and ancestors. In molecular phylogenies, the trilobus group is not the sister taxon of the ruber group. The ruber group clusters consistently together with the modern Globoturborotalita rubescens as a sister taxon. The re-analysis of the fossil record indicates that the first "Globigerinoides" in the late Oligocene are ancestral to the trilobus group, whereas the ruber group first appeared at the base of the Miocene with representatives distinct from the trilobus group. Therefore, polyphyly of the genus "Globigerinoides" as currently defined can only be avoided either by broadening the genus concept to include G. rubescens and a large number of fossil species without supplementary apertures, or if the trilobus group is assigned to a separate genus. Since the former is not feasible due to the lack of a clear diagnosis for such a broad genus, we erect a new genus Trilobatus for the trilobus group (type species Globigerina triloba Reuss) and amend Globoturborotalita and Globigerinoides to clarify morphology and wall textures of these genera. In the new concept, Trilobatus n. gen. is paraphyletic and gave rise to the Praeorbulina/Orbulina and Sphaeroidinellopsis/Sphaeroidinella lineages.
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Affiliation(s)
- Silvia Spezzaferri
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Michal Kucera
- Center for Marine Environmental Sciences MARUM, University of Bremen, Bremen, Germany
| | | | - Bridget Susan Wade
- Department of Earth Sciences, University College London, London, United Kingdom
| | - Sacha Rappo
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | | | - Raphaël Morard
- Center for Marine Environmental Sciences MARUM, University of Bremen, Bremen, Germany
| | - Claudio Stalder
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Morard R, Darling KF, Mahé F, Audic S, Ujiié Y, Weiner AKM, André A, Seears HA, Wade CM, Quillévéré F, Douady CJ, Escarguel G, de Garidel-Thoron T, Siccha M, Kucera M, de Vargas C. PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution. Mol Ecol Resour 2015; 15:1472-85. [DOI: 10.1111/1755-0998.12410] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Raphaël Morard
- Centre National de la Recherche Scientifique; UMR 7144; EPEP; Station Biologique de Roscoff; 29680 Roscoff France
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Station Biologique de Roscoff; 29680 Roscoff France
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Kate F. Darling
- School of GeoSciences; University of Edinburgh; Edinburgh EH9 3JW UK
- School of Geography and GeoSciences; University of St Andrews; Fife KY16 9AL UK
| | - Frédéric Mahé
- Department of Ecology; Technische Universität Kaiserslautern; 67663 Kaiserslautern Germany
| | - Stéphane Audic
- Centre National de la Recherche Scientifique; UMR 7144; EPEP; Station Biologique de Roscoff; 29680 Roscoff France
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Station Biologique de Roscoff; 29680 Roscoff France
| | - Yurika Ujiié
- Department of Biology; Shinshu University; Asahi3-1-1 Matsumoto Nagano 390-8621 Japan
| | - Agnes K. M. Weiner
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Aurore André
- CNRS UMR 5276; Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement; Université Claude Bernard Lyon 1; 69622 Villeurbanne France
- UFR Sciences Exactes et Naturelles; Université de Reims-Champagne-Ardenne; Campus Moulin de la Housse Batiment 18 51100 Reims France
| | - Heidi A. Seears
- School of Life Sciences; University of Nottingham; University Park Nottingham NG7 2RD UK
- Department of Biological Sciences; Lehigh University; Iacocca Hall 111 Research Drive Bethlehem PA 18105 USA
| | - Christopher M. Wade
- School of Life Sciences; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Frédéric Quillévéré
- CNRS UMR 5276; Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement; Université Claude Bernard Lyon 1; 69622 Villeurbanne France
| | - Christophe J. Douady
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1; ENTPE; CNRS; Université de Lyon; 6 rue Raphaël Dubois 69622 Villeurbanne France
- Institut Universitaire de France; 103 Boulevard Saint-Michel 75005 Paris France
| | - Gilles Escarguel
- CNRS UMR 5276; Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement; Université Claude Bernard Lyon 1; 69622 Villeurbanne France
| | | | - Michael Siccha
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences; University of Bremen; Leobener Strasse 28359 Bremen Germany
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique; UMR 7144; EPEP; Station Biologique de Roscoff; 29680 Roscoff France
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Station Biologique de Roscoff; 29680 Roscoff France
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30
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Significance and future role of microbial resource centers. Syst Appl Microbiol 2015; 38:258-65. [PMID: 25883055 DOI: 10.1016/j.syapm.2015.02.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 11/21/2022]
Abstract
Isolated strains constitute the basis for microbial systematics as well as for numerous applications in biotechnology, pharmacology, agronomy and public health. Microbial resource centers (mBRCs) are institutions capable of safeguarding, maintaining and distributing authenticated microbial strains, their genomic DNA and the associated data in a quality-controlled manner. They allow the deposit and distribution of type strains that form the basis of microbial taxonomy. Beyond taxonomy, deposited strains enable follow-up scientific studies and lead to a significantly improved recognition of scientific work. Considerable added value is generated through the labor-intensive steps of enrichment, enrichment screening, isolation, characterization, conservation and long-term storage of microbial strains. Here, a microbial strain is calculated to attain a value of 9836 Euro through its isolation and another 918 Euro through its deposit, adding up to a total value of 10,754 Euro. mBRCs provide a highly cost-effective way of preserving this value of microbial strains. A considerable future challenge of mBRCs will be to secure a larger fraction of strains that are isolated in research labs worldwide. mBRCs provide the expert knowledge and the cultivation and preservation skills crucial to access the large fraction of uncharted microbial diversity. mBRCs also provide the expertise and support the depositors of microbial resources to meet new legal challenges after implementation of the Nagoya Protocol. A suitable roadmap is described that allows mBRCs to meet the new demands emerging in science, technology and economy through an integration of novel technology, expansion of their duties and establishing an improved global mBRC network.
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31
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Comparison of Similar Arctic and Antarctic Morphotypes of Heterotrophic Protists Regarding their Genotypes and Ecotypes. Protist 2015; 166:42-57. [DOI: 10.1016/j.protis.2014.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 11/14/2014] [Accepted: 11/25/2014] [Indexed: 11/18/2022]
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32
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Weiner AKM, Weinkauf MFG, Kurasawa A, Darling KF, Kucera M, Grimm GW. Phylogeography of the tropical planktonic foraminifera lineage globigerinella reveals isolation inconsistent with passive dispersal by ocean currents. PLoS One 2014; 9:e92148. [PMID: 24663038 PMCID: PMC3963880 DOI: 10.1371/journal.pone.0092148] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/17/2014] [Indexed: 11/18/2022] Open
Abstract
Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale. Our data confirm the existence of multiple, well isolated genetic lineages. An analysis of their abundance and distribution indicates that our sampling is likely to approximate the actual total diversity. Unexpectedly, we observe an uneven allocation of cryptic diversity among the phylogenetic lineages. We show that this pattern is neither an artifact of sampling intensity nor a function of lineage age. Instead, we argue that it reflects an ongoing speciation process in one of the three major lineages. Surprisingly, four of the six genetic types in the hyperdiverse lineage are biogeographically restricted to the Indopacific. Their mutual co-occurrence and their hierarchical phylogenetic structure provide no evidence for an origin through sudden habitat fragmentation and their limitation to the Indopacific challenges the view of a global gene flow within the warm-water provinces. This phenomenon shows that passive dispersal is not sufficient to describe the distribution of plankton diversity. Rather, these organisms show differentiated distribution patterns shaped by species interactions and reflecting phylogenetic contingency with unique histories of diversification rates.
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Affiliation(s)
- Agnes K. M. Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- * E-mail:
| | - Manuel F. G. Weinkauf
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Atsushi Kurasawa
- Institute of Biogeosciences, Japanese Agency for Marine Earth Science and Technology, Yokosuka, Japan
| | - Kate F. Darling
- School of Geosciences and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Guido W. Grimm
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
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33
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Ezard THG, Thomas GH, Purvis A. Inclusion of a near-complete fossil record reveals speciation-related molecular evolution. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12089] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Thomas H. G. Ezard
- Centre for Biological Sciences; University of Southampton; Life Sciences Building 85, Highfield Campus; Southampton; SO17 1BJ; UK
| | - Gavin H. Thomas
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield; S10 2TN; UK
| | - Andy Purvis
- Department of Life Sciences; Imperial College London; Silwood Park Campus; Ascot; Berkshire; SL5 7PY; UK
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34
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Di Giuseppe G, Barbieri M, Vallesi A, Luporini P, Dini F. Phylogeographical pattern ofEuplotes nobilii, a protist ciliate with a bipolar biogeographical distribution. Mol Ecol 2013; 22:4029-37. [DOI: 10.1111/mec.12363] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/19/2013] [Accepted: 04/25/2013] [Indexed: 11/26/2022]
Affiliation(s)
| | | | - Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology; Department of Environmental Sciences; University of Camerino; 62032 Camerino MC Italy
| | - Pierangelo Luporini
- Laboratory of Eukaryotic Microbiology and Animal Biology; Department of Environmental Sciences; University of Camerino; 62032 Camerino MC Italy
| | - Fernando Dini
- Department of Biology; University of Pisa; 56126 Pisa Italy
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35
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Sul WJ, Oliver TA, Ducklow HW, Amaral-Zettler LA, Sogin ML. Marine bacteria exhibit a bipolar distribution. Proc Natl Acad Sci U S A 2013; 110:2342-7. [PMID: 23324742 PMCID: PMC3568360 DOI: 10.1073/pnas.1212424110] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial cosmopolitan dispersion hypothesis often invoked to explain distribution patterns driven by high connectivity of oceanographic water masses and widespread dispersal ability has never been rigorously tested. By using a global marine bacterial dataset and iterative matrix randomization simulation, we show that marine bacteria exhibit a significantly greater dispersal limitation than predicted by our null model using the "everything is everywhere" tenet with no dispersal limitation scenario. Specifically, marine bacteria displayed bipolar distributions (i.e., species occurring exclusively at both poles and nowhere else) significantly less often than in the null model. Furthermore, we observed fewer taxa present in both hemispheres but more taxa present only in a single hemisphere than expected under the null model. Each of these trends diverged further from the null expectation as the compared habitats became more geographically distant but more environmentally similar. Our meta-analysis supported a latitudinal gradient in bacterial diversity with higher richness at lower latitudes, but decreased richness toward the poles. Bacteria in the tropics also demonstrated narrower latitudinal ranges at lower latitudes and relatively larger ranges in higher latitudes, conforming to the controversial macroecological pattern of the "Rapoport rule." Collectively, our findings suggest that bacteria follow biogeographic patterns more typical of macroscopic organisms, and that dispersal limitation, not just environmental selection, likely plays an important role. Distributions of microbes that deliver critical ecosystem services, particularly those in polar regions, may be vulnerable to the same impacts that environmental stressors, climate warming, and degradation in habitat quality are having on biodiversity in animal and plant species.
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Affiliation(s)
- Woo Jun Sul
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Thomas A. Oliver
- Hawai’i Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744
| | - Hugh W. Ducklow
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA 02543; and
| | - Linda A. Amaral-Zettler
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
- Department of Geological Sciences, Brown University, Providence, RI 02912
| | - Mitchell L. Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
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36
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Assessing the role of cladogenesis in macroevolution by integrating fossil and molecular evidence. Proc Natl Acad Sci U S A 2013; 110:2904-9. [PMID: 23378632 DOI: 10.1073/pnas.1208302110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Assessing the extent to which population subdivision during cladogenesis is necessary for long-term phenotypic evolution is of fundamental importance in a broad range of biological disciplines. Differentiating cladogenesis from anagenesis, defined as evolution within a species, has generally been hampered by dating precision, insufficient fossil data, and difficulties in establishing a direct link between morphological changes detectable in the fossil record and biological species. Here we quantify the relative frequencies of cladogenesis and anagenesis for macroperforate planktic Foraminifera, which arguably have the most complete fossil record currently available, to address this question. Analyzing this record in light of molecular evidence, while taking into account the precision of fossil dating techniques, we estimate that the fraction of speciation events attributable to anagenesis is <19% during the Cenozoic era (last 65 Myr) and <10% during the Neogene period (last 23 Myr). Our central conclusion--that cladogenesis is the predominant mode by which new planktic Foraminifera taxa become established at macroevolutionary time scales--differs markedly from the conclusion reached in a recent study based solely on fossil data. These disparate findings demonstrate that interpretations of macroevolutionary dynamics in the fossil record can be fundamentally altered in light of genetic evidence.
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37
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Peters SE, Kelly DC, Fraass AJ. Oceanographic controls on the diversity and extinction of planktonic foraminifera. Nature 2013; 493:398-401. [PMID: 23302802 DOI: 10.1038/nature11815] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 11/29/2012] [Indexed: 11/09/2022]
Abstract
Understanding the links between long-term biological evolution, the ocean-atmosphere system and plate tectonics is a central goal of Earth science. Although environmental perturbations of many different kinds are known to have affected long-term biological evolution, particularly during major mass extinction events, the relative importance of physical environmental factors versus biological interactions in governing rates of extinction and origination through geological time remains unknown. Here we use macrostratigraphic data from the Atlantic Ocean basin to show that changes in global species diversity and rates of extinction among planktonic foraminifera have been linked to tectonically and climatically forced changes in ocean circulation and chemistry from the Jurassic period to the present. Transient environmental perturbations, such as those that occurred after the asteroid impact at the end of the Cretaceous period approximately 66 million years ago, and the Eocene/Oligocene greenhouse-icehouse transition approximately 34 million years ago, are superimposed on this general long-term relationship. Rates of species origination, by contrast, are not correlated with corresponding macrostratigraphic quantities, indicating that physiochemical changes in the ocean-atmosphere system affect evolution principally by driving the synchronous extinction of lineages that originated owing to more protracted and complex interactions between biological and environmental factors.
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Affiliation(s)
- Shanan E Peters
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin 53706, USA.
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38
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Herrera S, Shank TM, Sánchez JA. Spatial and temporal patterns of genetic variation in the widespread antitropical deep-sea coralParagorgia arborea. Mol Ecol 2012; 21:6053-67. [DOI: 10.1111/mec.12074] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/28/2012] [Accepted: 09/01/2012] [Indexed: 01/20/2023]
Affiliation(s)
| | - T. M. Shank
- Biology Department; Woods Hole Oceanographic Institution; 266 Woods Hole Road; Woods Hole; MA; 02543; USA
| | - J. A. Sánchez
- Laboratorio de Biologia Molecular Marina (BIOMMAR), Departamento Ciencias Biologicas; Universidad de los Andes; Carrera 1E No 18A - 10; Bogota; Colombia
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39
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Sato H, Tsujino R, Kurita K, Yokoyama K, Agata K. Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism. Mol Ecol 2012; 21:5599-612. [DOI: 10.1111/mec.12053] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Hirotoshi Sato
- Graduate School of Global Environmental Studies; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
| | - Riyou Tsujino
- Primate Research Institute; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
| | - Kazuki Kurita
- Laboratory of Systematic Zoology; Graduate School of Science; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
| | | | - Kiyokazu Agata
- Laboratory for Molecular Developmental Biology; Graduate School of Science; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
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Weiner A, Aurahs R, Kurasawa A, Kitazato H, Kucera M. Vertical niche partitioning between cryptic sibling species of a cosmopolitan marine planktonic protist. Mol Ecol 2012; 21:4063-73. [PMID: 22738662 DOI: 10.1111/j.1365-294x.2012.05686.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A large portion of the surface-ocean biomass is represented by microscopic unicellular plankton. These organisms are functionally and morphologically diverse, but it remains unclear how their diversity is generated. Species of marine microplankton are widely distributed because of passive transport and lack of barriers in the ocean. How does speciation occur in a system with a seemingly unlimited dispersal potential? Recent studies using planktonic foraminifera as a model showed that even among the cryptic genetic diversity within morphological species, many genetic types are cosmopolitan, lending limited support for speciation by geographical isolation. Here we show that the current two-dimensional view on the biogeography and potential speciation mechanisms in the microplankton may be misleading. By depth-stratified sampling, we present evidence that sibling genetic types in a cosmopolitan species of marine microplankton, the planktonic foraminifer Hastigerina pelagica, are consistently separated by depth throughout their global range. Such strong separation between genetically closely related and morphologically inseparable genetic types indicates that niche partitioning in marine heterotrophic microplankton can be maintained in the vertical dimension on a global scale. These observations indicate that speciation along depth (depth-parapatric speciation) can occur in vertically structured microplankton populations, facilitating diversification without the need for spatial isolation.
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Affiliation(s)
- Agnes Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany.
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41
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Jungblut AD, Vincent WF, Lovejoy C. Eukaryotes in Arctic and Antarctic cyanobacterial mats. FEMS Microbiol Ecol 2012; 82:416-28. [DOI: 10.1111/j.1574-6941.2012.01418.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/21/2012] [Accepted: 05/21/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Anne D. Jungblut
- Département de Biologie; Centre d'Études Nordiques (CEN); Institut de biologie intégrative et des systèmes (IBIS); Laval University; Quebec City; QC; Canada
| | - Warwick F. Vincent
- Département de Biologie; Centre d'Études Nordiques (CEN); Laval University; Quebec City; QC; Canada
| | - Connie Lovejoy
- Département de Biologie, Québec-Océan; Institut de biologie intégrative et des systèmes (IBIS); Laval University; Quebec City; QC; Canada
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42
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Seears HA, Darling KF, Wade CM. Ecological partitioning and diversity in tropical planktonic foraminifera. BMC Evol Biol 2012; 12:54. [PMID: 22507289 PMCID: PMC3361484 DOI: 10.1186/1471-2148-12-54] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 04/16/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Ecological processes are increasingly being viewed as an important mode of diversification in the marine environment, where the high dispersal potential of pelagic organisms, and a lack of absolute barriers to gene flow may limit the occurrence of allopatric speciation through vicariance. Here we focus on the potential role of ecological partitioning in the diversification of a widely distributed group of marine protists, the planktonic foraminifera. Sampling was conducted in the tropical Arabian Sea, during the southwest (summer) monsoon, when pronounced environmental conditions result in a strong disparity in temperature, salinity and productivity between distinct northern and southern water masses. RESULTS We uncovered extensive genetic diversity within the Arabian Sea planktonic foraminifera, identifying 13 morphospecies, represented by 20 distinct SSU rRNA genetic types. Several morphospecies/genetic types displayed non-random biogeographical distributions, partitioning between the northern and southern water masses, giving a strong indication of independent ecological adaptations. CONCLUSIONS We propose sea-surface primary productivity as the main factor driving the geographical segregation of Arabian Sea planktonic foraminifera, during the SW monsoon, with variations in symbiotic associations possibly playing a role in the specific ecological adaptations observed. Our findings suggest that ecological partitioning could be contributing to the high levels of 'cryptic' genetic diversity observed within the planktonic foraminifera, and support the view that ecological processes may play a key role in the diversification of marine pelagic organisms.
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Affiliation(s)
- Heidi A Seears
- School of Biology, University of Nottingham, Nottingham, UK
| | - Kate F Darling
- School of GeoSciences and Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Goetze E. Population differentiation in the open sea: insights from the pelagic copepod Pleuromamma xiphias. Integr Comp Biol 2012; 51:580-97. [PMID: 21940778 DOI: 10.1093/icb/icr104] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although a number of recent studies of marine holoplankton have reported significant genetic structure among populations, little is currently known about the biological and oceanographic processes that influence population connectivity in oceanic plankton. In order to examine how depth preferences influence dispersal in oceanic plankton, I characterized the genetic structure of a copepod with diel vertical migration (DVM) (Pleuromamma xiphias), throughout its global distribution, and compared these results to those expected given the interaction of this species' habitat depth with ocean circulation and bathymetry. Mitochondrial COI sequences from 651 individuals from 28 sites in the Indian, Pacific, and Atlantic Oceans revealed highly significant genetic differentiation both within and among ocean basins. Limited dispersal among distinct pelagic provinces seems to have played a major role in population differentiation in this species, with strong genetic breaks observed across known oceanographic fronts or current systems in all three ocean basins. The Indo-West Pacific (IWP) holds a highly distinct genetic population of this species that was sampled in both the western Pacific and eastern Indian Oceans. This suggests that the IWP does not act as a strong barrier to gene flow between basins, as expected, despite the relatively shallow water depth (<200 m) and vertically extensive (>400 m) diel migration of this species. A pattern of isolation by distance was observed in the Indian Ocean with genetic differentiation among samples down to spatial scales of ∼800 km, indicating that realized dispersal in P. xiphias occurs over much smaller spatial scales than in previously reported oceanic holoplankton. Given its highly regionalized population genetic structure, P. xiphias may have some capacity to adapt to local oceanographic conditions, and it should not be assumed that populations of this species in distinct pelagic biomes will respond in the same way to shared physical or climatic forcing.
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Affiliation(s)
- Erica Goetze
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales. ISME JOURNAL 2011; 6:713-23. [PMID: 22071346 DOI: 10.1038/ismej.2011.138] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000-3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales.
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Morard R, Quillévéré F, Douady CJ, de Vargas C, de Garidel-Thoron T, Escarguel G. Worldwide genotyping in the planktonic foraminifer Globoconella inflata: implications for life history and paleoceanography. PLoS One 2011; 6:e26665. [PMID: 22028935 PMCID: PMC3197684 DOI: 10.1371/journal.pone.0026665] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/30/2011] [Indexed: 11/19/2022] Open
Abstract
The planktonic foraminiferal morpho-species Globoconella inflata is widely used as a stratigraphic and paleoceanographic index. While G. inflata was until now regarded as a single species, we show that it rather constitutes a complex of two pseudo-cryptic species. Our study is based on SSU and ITS rDNA sequence analyses and genotyping of 497 individuals collected at 49 oceanic stations covering the worldwide range of the morpho-species. Phylogenetic analyses unveil the presence of two divergent genotypes. Type I inhabits transitional and subtropical waters of both hemispheres, while Type II is restricted to the Antarctic subpolar waters. The two genetic species exhibit a strictly allopatric distribution on each side of the Antarctic Subpolar Front. On the other hand, sediment data show that G. inflata was restricted to transitional and subtropical environments since the early Pliocene, and expanded its geographic range to southern subpolar waters ∼700 kyrs ago, during marine isotopic stage 17. This datum may correspond to a peripatric speciation event that led to the partition of an ancestral genotype into two distinct evolutionary units. Biometric measurements performed on individual G. inflata from plankton tows north and south of the Antarctic Subpolar Front indicate that Types I and II display slight but significant differences in shell morphology. These morphological differences may allow recognition of the G. inflata pseudo-cryptic species back into the fossil record, which in turn may contribute to monitor past movements of the Antarctic Subpolar Front during the middle and late Pleistocene.
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Affiliation(s)
- Raphaël Morard
- CNRS UMR 5276 Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France.
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Agatha S. Global diversity of aloricate Oligotrichea (Protista, Ciliophora, Spirotricha) in marine and brackish sea water. PLoS One 2011; 6:e22466. [PMID: 21853034 PMCID: PMC3154192 DOI: 10.1371/journal.pone.0022466] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oligotrichids and choreotrichids are ciliate taxa contributing to the multi-step microbial food web and episodically dominating the marine microzooplankton. The global diversity and distribution of aloricate Oligotrichea are unknown. Here, the geographic ranges of the 141 accepted species and their synonyms in marine and brackish sea water are analyzed, using hundreds of taxonomical and ecological studies; the quality of the records is simultaneously evaluated. The aloricate Oligotrichea match the moderate endemicity model, i.e., the majority (94) of morphospecies has a wide, occasionally cosmopolitan distribution, while 47 morphospecies show biogeographic patterns: they are restricted to single geographic regions and probably include 12 endemic morphospecies. These endemics are found in the Antarctic, North Pacific, and Black Sea, whereas the "flagship" species Strombidinopsis cercionis is confined to the Caribbean Sea. Concerning genera, again several geographic patterns are recognizable. The species richness is distinctly lower in the southern hemisphere than in the northern, ranging from nine morphospecies in the South Pacific to 95 in the North Atlantic; however, this pattern is probably caused by undersampling. Since the loss of species might affect higher trophical levels substantially, the aloricate Oligotrichea should not any longer be ignored in conservation issues. The ecophysiological diversity is considerably larger than the morphological, and even tops the richness of SSrRNA and ITS haplotypes, indicating that probably more than 83-89% of the diversity in aloricate Oligotrichea are unknown. The huge challenge to discover all these species can only be managed by combining the expertises of morphological taxonomists, molecular biologists, ecologists, and physiologists.
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Affiliation(s)
- Sabine Agatha
- Department of Organismic Biology, University of Salzburg, Salzburg, Austria.
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Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 2011; 12:2998-3006. [PMID: 20561020 DOI: 10.1111/j.1462-2920.2010.02277.x] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The severe environmental stresses of the Arctic may have promoted unique soil bacterial communities compared with those found in lower latitude environments. Here, we present a comprehensive analysis of the biogeography of soil bacterial communities in the Arctic using a high resolution bar-coded pyrosequencing technique. We also compared arctic soils with soils from a wide range of more temperate biomes to characterize variability in soil bacterial communities across the globe. We show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites, suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining community-level differences. Furthermore, bacterial community composition had similar levels of variability, richness and phylogenetic diversity within arctic soils as across soils from a wide range of lower latitudes, strongly suggesting a common diversity structure within soil bacterial communities around the globe. These results contrast with the well-established latitudinal gradients in animal and plant diversity, suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro-organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.
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Affiliation(s)
- Haiyan Chu
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
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48
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Antarctic and Arctic populations of the ciliate Euplotes nobilii show common pheromone-mediated cell-cell signaling and cross-mating. Proc Natl Acad Sci U S A 2011; 108:3181-6. [PMID: 21300903 DOI: 10.1073/pnas.1019432108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wild-type strains of the protozoan ciliate Euplotes collected from different locations on the coasts of Antarctica, Tierra del Fuego and the Arctic were taxonomically identified as the morpho-species Euplotes nobilii, based on morphometric and phylogenetic analyses. Subsequent studies of their sexual interactions revealed that mating combinations of Antarctic and Arctic strains form stable pairs of conjugant cells. These conjugant pairs were isolated and shown to complete mutual gene exchange and cross-fertilization. The biological significance of this finding was further substantiated by demonstrating that close homology exists among the three-dimensional structures determined by NMR of the water-borne signaling pheromones that are constitutively secreted into the extracellular space by these interbreeding strains, in which these molecules trigger the switch between the growth stage and the sexual stage of the life cycle. The fact that Antarctic and Arctic E. nobilii populations share the same gene pool and belong to the same biological species provides new support to the biogeographic model of global distribution of eukaryotic microorganisms, which had so far been based exclusively on studies of morphological and phylogenetic taxonomy.
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49
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Lowe CD, Montagnes DJS, Martin LE, Watts PC. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae) uncovered by microsatellite loci. PLoS One 2010; 5:e15557. [PMID: 21203414 PMCID: PMC3009739 DOI: 10.1371/journal.pone.0015557] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/12/2010] [Indexed: 11/18/2022] Open
Abstract
Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites) has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e)) of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST) values indicated weak to moderate population sub-division (0.01-0.12), but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.
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Affiliation(s)
- Chris D Lowe
- School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom.
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50
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Göker M, Grimm GW, Auch AF, Aurahs R, Kučera M. A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA. Evol Bioinform Online 2010; 6:97-112. [PMID: 21037964 PMCID: PMC2964048 DOI: 10.4137/ebo.s5504] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts.
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Affiliation(s)
- Markus Göker
- German Collection of Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Guido W. Grimm
- Swedish Museum of Natural History, Box 50007, Stockholm, Sweden
| | - Alexander F. Auch
- Center for Bioinformatics Tübingen, Eberhard Karls University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Ralf Aurahs
- Institute of Geosciences, Eberhard Karls University of Tübingen, Sigwartstraße 10, 72076 Tübingen, Germany
| | - Michal Kučera
- Institute of Geosciences, Eberhard Karls University of Tübingen, Sigwartstraße 10, 72076 Tübingen, Germany
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