How Many Species Are There on Earth and in the Ocean?, PLoS Biology, vol.93, issue.8, p.1001127, 2011. ,
DOI : 10.1371/journal.pbio.1001127.s004
Imagining Sisyphus happy: DNA barcoding and the unnamed majority, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.86, issue.1702, p.20150329, 2016. ,
DOI : 10.1016/j.ecss.2008.04.014
Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera, PLoS ONE, vol.71, issue.12, pp.1-8, 2013. ,
DOI : 10.1371/journal.pone.0056739.s007
Wide Occurrence of SSU rDNA Intragenomic Polymorphism in Foraminifera and its Implications for Molecular Species Identification, Protist, vol.165, issue.5, pp.645-661, 2014. ,
DOI : 10.1016/j.protis.2014.07.006
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucleic Acids Research, vol.20, issue.D1, pp.597-604, 2013. ,
DOI : 10.1093/bioinformatics/bth226
URL : https://hal.archives-ouvertes.fr/hal-01253994
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.35, issue.D1, pp.590-596, 2013. ,
DOI : 10.1093/nar/gkl856
BARCODING: bold: The Barcode of Life Data System (http://www.barcodinglife.org), Molecular Ecology Notes, vol.360, issue.3, pp.355-364, 2007. ,
DOI : 10.1101/gr.8.3.175
Microbial diversity in the deep sea and the underexplored "rare biosphere", Proc. Natl. Acad. Sci. USA 103, pp.12115-12135, 2006. ,
DOI : 10.1093/bioinformatics/18.11.1546
Patterns of Rare and Abundant Marine Microbial Eukaryotes, Current Biology, vol.24, issue.8, pp.813-834, 2014. ,
DOI : 10.1016/j.cub.2014.02.050
URL : https://hal.archives-ouvertes.fr/hal-01149637
Eukaryotic plankton diversity in the sunlit ocean, Science, vol.48, issue.1, pp.1261605-1261605, 2015. ,
DOI : 10.1111/j.1529-8817.2012.01150.x
Benthic protists: the under-charted majority, FEMS Microbiology Ecology, vol.6, issue.8, p.120, 2016. ,
DOI : 10.1111/mec.12640
URL : https://hal.archives-ouvertes.fr/hal-01383722
Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses, Nucleic Acids Research, vol.39, issue.9, pp.1-9, 2012. ,
DOI : 10.1073/pnas.96.12.6820
Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing, PLoS ONE, vol.8, issue.1010, p.104297, 2014. ,
DOI : 10.1371/journal.pone.0104297.s008
URL : https://hal.archives-ouvertes.fr/hal-01100668
UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.63, issue.Pt 5, pp.2194-200, 2011. ,
DOI : 10.1099/13500872-142-5-1107
Scraping the bottom of the barrel: Are rare high throughput sequences artifacts? Fungal Ecol, pp.221-225, 2015. ,
Parsing ecological signal from noise in next generation amplicon sequencing, New Phytologist, vol.16, issue.4, pp.1389-1393, 2015. ,
DOI : 10.1111/1462-2920.12390
Protistan community analysis: key findings of a large-scale molecular sampling, The ISME Journal, vol.51, issue.9, pp.1-1110, 2016. ,
DOI : 10.1111/j.1462-2920.2012.02797.x
Insidious effects of sequencing errors on perceived diversity in molecular surveys, New Phytologist, vol.282, issue.4, pp.916-918, 2010. ,
DOI : 10.1111/j.1469-8137.2010.03473.x
Accurate multiplexing and filtering for high-throughput amplicon-sequencing, Nucleic Acids Research, vol.14, issue.5, pp.2513-2524, 2015. ,
DOI : 10.1073/pnas.1002355107
URL : https://hal.archives-ouvertes.fr/hal-01279130
The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes, Proc. Natl. Acad. Sci. USA 101, pp.8066-71, 2004. ,
DOI : 10.1666/0094-8373(2000)026<0360:TAITNE>2.0.CO;2
The evolution of early Foraminifera, Proc. Natl. Acad. Sci. USA, pp.11494-11502, 2003. ,
DOI : 10.1126/science.197.4298.55
The search for the origin of the planktic Foraminifera, Journal of the Geological Society, vol.160, issue.3, pp.341-343, 2003. ,
DOI : 10.1144/0016-764903-003
Benthic origin and earliest evolution of the first planktonic foraminifera after the Cretaceous/Palaeogene boundary mass extinction, Historical Biology, vol.12, issue.1, pp.25-42, 2017. ,
DOI : 10.1016/j.marmicro.2008.09.003
Caught in the act: anatomy of an ongoing benthic?planktonic transition in a marine protist, J. Plankton Res, vol.39, pp.436-449, 2017. ,
Planktic foraminiferal molecular evolution and their polyphyletic origins from benthic taxa, Marine Micropaleontology, vol.30, issue.4, pp.251-266, 1997. ,
DOI : 10.1016/S0377-8398(96)00057-6
A revised cenozoic geochronology and chronostratigraphy. Geochronology, Time Scales, and Global Stratigraphic Correlation 54, pp.129-212, 1995. ,
Proxies in Late Cenozoic Paleoceanography, Developments in Marine Geology, vol.1, 2007. ,
Ecology of Planktonic Foraminifera and Biogeographic Patterns of Life and Fossil Assemblages in the Indian Ocean, Micropaleontology, vol.23, issue.4, pp.369-414, 1977. ,
DOI : 10.2307/1485406
Global analysis of seasonality in the shell flux of extant planktonic Foraminifera, Biogeosciences, vol.12, issue.7, pp.2207-2226, 2015. ,
DOI : 10.5194/bg-12-2207-2015-supplement
Multiproxy approach for the reconstruction of the glacial ocean surface (MARGO), Quaternary Science Reviews, vol.24, issue.7-9, pp.813-819, 2005. ,
DOI : 10.1016/j.quascirev.2004.07.017
Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera, Systematic Biology, vol.64, issue.5, pp.925-940, 2016. ,
DOI : 10.1093/bioinformatics/btt499
URL : https://hal.archives-ouvertes.fr/hal-01368819
The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes, Marine Micropaleontology, vol.67, issue.3-4, pp.216-238, 2008. ,
DOI : 10.1016/j.marmicro.2008.01.009
: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution, Molecular Ecology Resources, vol.9, issue.6, pp.1472-1485, 2015. ,
DOI : 10.1371/journal.pone.0108793
A Holistic Approach to Marine Eco-Systems Biology, PLoS Biology, vol.6, issue.10, p.1001177, 2011. ,
DOI : 10.1371/journal.pbio.1001177.g002
URL : https://hal.archives-ouvertes.fr/hal-00691580
Open science resources for the discovery and analysis of Tara Oceans data, Scientific Data, vol.43, issue.26, p.150023, 2015. ,
DOI : 10.1146/annurev-marine-120308-080950
URL : https://hal.archives-ouvertes.fr/hal-01253984
Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record, Journal of Molecular Evolution, vol.45, issue.3, pp.285-294, 1997. ,
DOI : 10.1007/PL00006232
Worldwide Genotyping in the Planktonic Foraminifer Globoconella inflata: Implications for Life History and Paleoceanography, PLoS ONE, vol.6, issue.10, p.26665, 2011. ,
DOI : 10.1371/journal.pone.0026665.s002
URL : https://hal.archives-ouvertes.fr/hal-00657029
Swarm: robust and fast clustering method for amplicon-based studies PrePrints PrePrints, 2014. ,
Molecular versus Taxonomic Rates of Evolution in Planktonic Foraminifera, Molecular Phylogenetics and Evolution, vol.9, issue.3, pp.463-469, 1998. ,
DOI : 10.1006/mpev.1998.0491
Improved tools for biological sequence comparison., Proc. Natl. Acad. Sci. USA, pp.2444-2448, 1988. ,
DOI : 10.1073/pnas.85.8.2444
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.25, issue.9, pp.772-780, 2013. ,
DOI : 10.1093/bioinformatics/btp033
New supraordinal classification of Foraminifera: Molecules meet morphology, Marine Micropaleontology, vol.100, pp.1-10, 2013. ,
DOI : 10.1016/j.marmicro.2013.04.002
8:2539 | DOI:10.1038/s41598-018-20833-z 45, jModelTest 2: more models, new heuristics and parallel computing, pp.772-772, 2012. ,
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.174, issue.3, pp.307-321, 2010. ,
DOI : 10.1093/bioinformatics/17.4.383
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Research, vol.311, issue.5765, pp.475-478, 2011. ,
DOI : 10.1126/science.1123061
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences, Bioinformatics and Biology Insights, vol.3, pp.155-177, 2009. ,
DOI : 10.4137/BBI.S3334
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA, Evolutionary Bioinformatics, vol.6, pp.97-112, 2010. ,
DOI : 10.4137/EBO.S5504
SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications, PLoS ONE, vol.17, issue.8, p.104641, 2014. ,
DOI : 10.1371/journal.pone.0104641.s005
Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity, Journal of Eukaryotic Microbiology, vol.22, issue.2, pp.185-192, 2012. ,
DOI : 10.1093/nar/22.22.4673
Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing, The ISME Journal, vol.52, issue.10, pp.1823-1833, 2012. ,
DOI : 10.1016/j.femsec.2004.10.006
URL : https://hal.archives-ouvertes.fr/hal-01258237
General Patterns of Diversity in Major Marine Microeukaryote Lineages, PLoS ONE, vol.2, issue.2, p.57170, 2013. ,
DOI : 10.1371/journal.pone.0057170.s008
URL : https://hal.archives-ouvertes.fr/hal-01253995
ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Molecular Ecology, vol.75, issue.8, pp.1864-1877, 2012. ,
DOI : 10.1128/AEM.00748-09
URL : https://hal.archives-ouvertes.fr/hal-00704914
Relationship between morphological taxonomy and molecular divergence within Crustacea: Proposal of a molecular threshold to help species delimitation, Molecular Phylogenetics and Evolution, vol.40, issue.2, pp.435-482, 2006. ,
DOI : 10.1016/j.ympev.2006.03.014
Paleontological statistics software package for education and data analysis, Palaeontol. Electron, vol.4, pp.9-18, 2001. ,
Biogeography and diversity of Collodaria (Radiolaria) in the global ocean Biogeography and diversity of Collodaria (Radiolaria) in the global ocean, 2017. ,
Censusing marine eukaryotic diversity in the twenty-first century, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.44, issue.1702, p.20150331, 2016. ,
DOI : 10.1525/bio.2013.63.5.8
Planktonic foraminiferal ontogeny and new perspectives for micropalaeontology, Nature, vol.11, issue.6048, pp.50-52, 1986. ,
DOI : 10.1038/319050a0
TRADITIONAL AND EMERGING GEOCHEMICAL PROXIES IN FORAMINIFERA, The Journal of Foraminiferal Research, vol.40, issue.2, pp.165-192, 2010. ,
DOI : 10.2113/gsjfr.40.2.165
Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution, Frontiers in Marine Science, vol.332, pp.1-15, 2016. ,
DOI : 10.1126/science.1203163
URL : https://hal.archives-ouvertes.fr/hal-01420794
Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities, PLOS ONE, vol.112, issue.2, pp.1-26, 2015. ,
DOI : 10.1371/journal.pone.0117562.s022
Extreme Diversity of Diplonemid Eukaryotes in the Ocean, Current Biology, vol.26, issue.22, pp.3060-3065, 2016. ,
DOI : 10.1016/j.cub.2016.09.031
First-order estimate of the planktic foraminifer biomass in the modern ocean, Earth System Science Data, vol.4, issue.1, pp.75-89, 2012. ,
DOI : 10.5194/essd-4-75-2012
World Ocean Atlas 2013, Temperature. NOAA Atlas NESDIS, vol.1, issue.73, p.40, 2013. ,
ggplot2: Elegant Graphics for Data Analysis, 2009. ,
R: A language and environment for statistical computing. R Foundation for Statistical Computing Available at: http://www.r-project, 2014. ,