1
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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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2
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Weiner AKM, Sehein T, Cote-L’Heureux A, Sleith RS, Greco M, Malekshahi C, Ryan-Embry C, Ostriker N, Katz LA. Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes. Evolution 2023; 77:2472-2483. [PMID: 37672006 PMCID: PMC10629589 DOI: 10.1093/evolut/qpad158] [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: 08/03/2022] [Revised: 08/13/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies-Hyalosphenia papilio and Hyalosphenia elegans-of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Taylor Sehein
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Robin S Sleith
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Mattia Greco
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Clara Malekshahi
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Chase Ryan-Embry
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Naomi Ostriker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, United States
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3
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Greco M, Morard R, Darling K, Kucera M. Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera. PeerJ 2023; 11:e15255. [PMID: 37123000 PMCID: PMC10143585 DOI: 10.7717/peerj.15255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
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Affiliation(s)
- Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Institut de Ciències del Mar (ICM), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Raphaël Morard
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kate Darling
- School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Michal Kucera
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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4
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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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5
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Weinkauf MFG, Siccha M, Weiner AKM. Reproduction dynamics of planktonic microbial eukaryotes in the open ocean. J R Soc Interface 2022; 19:20210860. [PMID: 35167772 PMCID: PMC8847003 DOI: 10.1098/rsif.2021.0860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Understanding the biology of reproduction of an organismal lineage is important for retracing key evolutionary processes, yet gaining detailed insights often poses major challenges. Planktonic Foraminifera are globally distributed marine microbial eukaryotes and important contributors to the global carbon cycle. They cannot routinely be cultured under laboratory conditions across generations, and thus details of their life cycle remain incomplete. The production of flagellated gametes has long been taken as an indication of exclusively sexual reproduction, but recent research suggests the existence of an additional asexual generation in the life cycle. To gain a better understanding of the reproductive biology of planktonic Foraminifera, we applied a dynamic, individual-based modelling approach with parameters based on laboratory and field observations to test if sexual reproduction is sufficient for maintaining viable populations. We show that temporal synchronization and potentially spatial concentration of gamete release seems inevitable for maintenance of the population under sexual reproduction. We hypothesize that sexual reproduction is likely beneficial during the adaptation to new environments, while population sustenance in stable environments can be ensured through asexual reproduction.
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Affiliation(s)
- Manuel F G Weinkauf
- Institute of Geology and Palaeontology, Univerzita Karlova, 128 43 Praha, Czech Republic.,Department of Earth Sciences, Université de Genève, 1205 Genève, Switzerland
| | - Michael Siccha
- Center for Marine Environmental Sciences (MARUM), Universität Bremen, 28359 Bremen, Germany
| | - Agnes K M Weiner
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, 5007 Bergen, Norway
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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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Weiner AKM, Katz LA. Epigenetics as Driver of Adaptation and Diversification in Microbial Eukaryotes. Front Genet 2021; 12:642220. [PMID: 33796133 PMCID: PMC8007921 DOI: 10.3389/fgene.2021.642220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
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8
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Rillo MC, Miller CG, Kucera M, Ezard THG. Intraspecific size variation in planktonic foraminifera cannot be consistently predicted by the environment. Ecol Evol 2020; 10:11579-11590. [PMID: 33144985 PMCID: PMC7593196 DOI: 10.1002/ece3.6792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 11/25/2022] Open
Abstract
The size structure of plankton communities is an important determinant of their functions in marine ecosystems. However, few studies have quantified how organism size varies within species across biogeographical scales. Here, we investigate how planktonic foraminifera, a ubiquitous zooplankton group, vary in size across the tropical and subtropical oceans of the world. Using a recently digitized museum collection, we measured shell area of 3,799 individuals of nine extant species in 53 seafloor sediments. We first analyzed potential size biases in the collection. Then, for each site, we obtained corresponding local values of mean annual sea-surface temperature (SST), net primary productivity (NPP), and relative abundance of each species. Given former studies, we expected species to reach largest shell sizes under optimal environmental conditions. In contrast, we observe that species differ in how much their size variation is explained by SST, NPP, and/or relative abundance. While some species have predictable size variation given these variables (Trilobatus sacculifer, Globigerinoides conglobatus, Globigerinella siphonifera, Pulleniatina obliquiloculata, Globorotalia truncatulinoides), other species show no relationships between size and the studied covariates (Globigerinoides ruber, Neogloboquadrina dutertrei, Globorotalia menardii, Globoconella inflata). By incorporating intraspecific variation and sampling broader geographical ranges compared to previous studies, we conclude that shell size variation in planktonic foraminifera species cannot be consistently predicted by the environment. Our results caution against the general use of size as a proxy for planktonic foraminifera environmental optima. More generally, our work highlights the utility of natural history collections and the importance of studying intraspecific variation when interpreting macroecological patterns.
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Affiliation(s)
- Marina C. Rillo
- Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of Southampton Waterfront CampusSouthamptonUK
- Department of Earth SciencesNatural History MuseumLondonUK
- Center for Marine Environmental SciencesUniversity of BremenBremenGermany
| | | | - Michal Kucera
- Center for Marine Environmental SciencesUniversity of BremenBremenGermany
| | - Thomas H. G. Ezard
- Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of Southampton Waterfront CampusSouthamptonUK
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9
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Prazeres M, Morard R, Roberts TE, Doo SS, Jompa J, Schmidt C, Stuhr M, Renema W, Kucera M. High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef-dwelling calcifier. Ecol Evol 2020; 10:5976-5989. [PMID: 32607205 PMCID: PMC7319125 DOI: 10.1002/ece3.6335] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo-West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological-scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation.
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Affiliation(s)
- Martina Prazeres
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
| | | | - T. Edward Roberts
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
| | - Steve S. Doo
- Leibniz Centre for Tropical Marine ResearchBremenGermany
- Department of BiologyCalifornia State UniversityNorthridgeCAUSA
| | | | | | - Marleen Stuhr
- Leibniz Centre for Tropical Marine ResearchBremenGermany
- Interuniversity Institute for Marine Sciences (IUI)EilatIsrael
- Bar‐Ilan University (BIU)Ramat GanIsrael
| | - Willem Renema
- Marine Biodiversity GroupNaturalis Biodiversity CenterLeidenThe Netherlands
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10
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Zehady AK, Fordham BG, Ogg JG. Integrated species-phenon trees: visualizing infraspecific diversity within lineages. Sci Rep 2019; 9:18968. [PMID: 31831804 PMCID: PMC6908663 DOI: 10.1038/s41598-019-55435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/25/2019] [Indexed: 12/03/2022] Open
Abstract
The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species-phenon tree merges ancestor-descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into "species boxes" and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent-child hierarchy in the integrated tree has been the progressive population of a species-phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others' important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.
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Affiliation(s)
- Abdullah Khan Zehady
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA
| | - Barry G Fordham
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia.
| | - James G Ogg
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Chengdu University of Technology, Chengdu, Sichuan, China
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11
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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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12
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Dagamac NHA, Rojas C, Novozhilov YK, Moreno GH, Schlueter R, Schnittler M. Speciation in progress? A phylogeographic study among populations of Hemitrichia serpula (Myxomycetes). PLoS One 2017; 12:e0174825. [PMID: 28414791 PMCID: PMC5393559 DOI: 10.1371/journal.pone.0174825] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 11/19/2022] Open
Abstract
Myxomycetes (plasmodial slime molds, Amoebozoa) are often perceived as widely distributed, confounding to the “everything is everywhere” hypothesis. To test if gene flow within these spore-dispersed protists is restricted by geographical barriers, we chose the widespread but morphologically unmistakable species Hemitrichia serpula for a phylogeographic study. Partial sequences from nuclear ribosomal RNA genes (SSU) revealed 40 ribotypes among 135 specimens, belonging to three major clades. Each clade is dominated by specimens from a certain region and by one of two morphological varieties which can be differentiated by SEM micrographs. Partial sequences of the protein elongation factor 1 alpha (EF1A) showed each clade to possess a unique combination of SSU and EF1A genotypes. This pattern is best explained assuming the existence of several putative biospecies dominating in a particular geographical region. However, occasional mismatches between molecular data and morphological characters, but as well heterogeneous SSU and heterozygous EF1A sequences, point to ongoing speciation. Environmental niche models suggest that the putative biospecies are rather restricted by geographical barriers than by macroecological conditions. Like other protists, myxomycetes seem to follow the moderate endemicity hypothesis and are in active speciation, which is most likely shaped by limited gene flow and reproductive isolation.
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Affiliation(s)
- Nikki Heherson A. Dagamac
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Soldmannstr. 15, Greifswald, Germany
- * E-mail: (NHAD); (MS)
| | - Carlos Rojas
- Engineering Research Institute and Department of Agricultural Engineering, University of Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Yuri K. Novozhilov
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, St. Petersburg, Russia
| | - Gabriel H. Moreno
- Departamento de Biología Vegetal, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - Rabea Schlueter
- Laboratory of Electron Microscopy, Institute of Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Soldmannstr. 15, Greifswald, Germany
- * E-mail: (NHAD); (MS)
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13
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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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14
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Morard R, Escarguel G, Weiner AKM, André A, Douady CJ, Wade CM, Darling KF, Ujiié Y, Seears HA, Quillévéré F, de Garidel-Thoron T, de Vargas C, Kucera M. Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera. Syst Biol 2016; 65:925-40. [PMID: 27073250 DOI: 10.1093/sysbio/syw031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/04/2016] [Indexed: 11/12/2022] Open
Abstract
Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany,
| | - Gilles Escarguel
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Agnes K M Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, Japan Agency for Marine Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa, Japan
| | - Aurore André
- Université de Reims-Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, Batiment 18, 51100 REIMS, France
| | - Christophe J Douady
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France, Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Christopher M Wade
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - 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
| | - Yurika Ujiié
- Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Heidi A Seears
- Department of Biology, Gilmer Hall, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904, USA
| | - Frédéric Quillévéré
- Univ Lyon, Université Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France
| | - Thibault de Garidel-Thoron
- Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, Centre National de la Recherche Scientifique, et Aix-Marseille Université, Aix-en-Provence, France
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France, and Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
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15
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Schiffer PH, Herbig HG. Endorsing Darwin: global biogeography of the epipelagic goose barnaclesLepas spp. (Cirripedia, Lepadomorpha) proves cryptic speciation. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philipp H. Schiffer
- Institute for Genetics; University of Cologne; Zülpicher Strasse 47 D-50674 Köln Germany
- EMBL; Meyerhofstraße 1 D-69117 Heidelberg Germany
| | - Hans-Georg Herbig
- Institute of Geology and Mineralogy; University of Cologne; Zülpicher Strasse 49a D-50674 Köln Germany
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16
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Ujiié Y, Ishitani Y. Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans. PLoS One 2016; 11:e0148847. [PMID: 26886349 PMCID: PMC4757448 DOI: 10.1371/journal.pone.0148847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/25/2016] [Indexed: 11/18/2022] Open
Abstract
Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world’s oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.
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Affiliation(s)
- Yurika Ujiié
- Department of Biology, Shinshu University, Matsumoto, Nagano, Japan
- * E-mail:
| | - Yoshiyuki Ishitani
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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17
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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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18
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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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19
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The Interdependency of the Morphological Variations of the Planktonic Foraminiferal Species Globigerina bulloides in Surface Sediments on the Environmental Parameters of the Southwestern Indian Ocean. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:621479. [PMID: 27379333 PMCID: PMC4897346 DOI: 10.1155/2014/621479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/13/2014] [Accepted: 09/25/2014] [Indexed: 12/02/2022]
Abstract
18 surface sediment samples collected from a north-south transect along the Indian Ocean have been analyzed for planktonic Foraminifera content. Among the other planktonic foraminiferal faunas, Globigerina bulloides was present substantially in all samples. Census data of G. bulloides were measured for different parameters (average size, mean proloculus size, coiling direction, and number of chambers) and a Q-mode cluster analysis was applied on these data. Samples were segregated into two homogeneous clusters, each reflecting particular environmental conditions. Two clusters are as follows: (1) Cluster A, comprised of 6 samples and characterized by the highest range of foraminiferal and ecological parameters, except sea surface temperature and salinity which shows the lowest range, and (2) Cluster B, comprised of 12 samples and characterized by the lowest range of foraminiferal parameters and ecological parameters, except sea surface temperature and salinity which shows the highest range. The study suggests that the ecological parameters are the governing factors for the morphological characteristics of planktonic foraminiferal species G. bulloides.
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