@article {bendif_rapid_2023,
	title = {Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton},
	journal = {The ISME Journal},
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	pages = {1{\textendash}11},
	abstract = {Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (\textasciitilde140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.},
	keywords = {Microbial biooceanography, phylogenomics, population genetics, rcc1212, RCC1216, rcc1220, RCC1239, RCC1240, RCC1242, RCC1245, rcc1252, RCC1253, RCC1266, RCC1304, rcc1731, RCC1754, RCC1813, RCC1823, rcc1824, RCC1830, RCC1838, RCC1840, RCC1853, RCC1856, RCC3746, RCC4027, RCC4028, RCC4030, RCC5134, RCC5137, RCC5141, RCC6381, RCC6421, RCC6427, RCC6566, RCC6660, RCC6666, RCC911, RCC963},
	issn = {1751-7370},
	doi = {10.1038/s41396-023-01365-5},
	url = {https://www.nature.com/articles/s41396-023-01365-5},
	author = {Bendif, El Mahdi and Probert, Ian and Archontikis, Odysseas A. and Young, Jeremy R. and Beaufort, Luc and Rickaby, Rosalind E. and Filatov, Dmitry}
}
@article {zhang_stimulating_2023,
	title = {Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte},
	journal = {New Phytologist},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19376},
	abstract = {Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv/Fm) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation.},
	keywords = {chromium, Photosynthesis, phytoplankton, proteomics, RCC1, RCC1242, trace metal},
	issn = {1469-8137},
	doi = {10.1111/nph.19376},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19376},
	author = {Zhang, Qiong and Charles, Philip D. and Bendif, El Mahdi and Hester, Svenja S. and Mohammad, Shabaz and Rickaby, Rosalind E. M.}
}
@article {filatov_mode_2021,
	title = {The mode of speciation during a recent radiation in open-ocean phytoplankton},
	journal = {Current Biology},
	year = {2021},
	month = {oct},
	abstract = {Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.},
	keywords = {phytoplankton, population genetic modeling, rcc1212, rcc1238, RCC1239, RCC1253, RCC1281, RCC1296, RCC1310, RCC1314, RCC1562, RCC1836, RCC3370, RCC3711, RCC3733, RCC3862, RCC3898, RCC4002, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, RCC5119, RCC5134, RCC5137, RCC5141, RCC6566, RCC6730, secondary contact, sequence polymorphism, speciation},
	issn = {0960-9822},
	doi = {10.1016/j.cub.2021.09.073},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982221013415},
	author = {Filatov, Dmitry A. and Bendif, El Mahdi and Archontikis, Odysseas A. and Hagino, Kyoko and Rickaby, Rosalind E. M.}
}
@article {bendif_repeated_2019,
	title = {Repeated species radiations in the recent evolution of the key marine phytoplankton lineage Gephyrocapsa},
	journal = {Nature Communications},
	volume = {10},
	number = {1},
	year = {2019},
	pages = {4234},
	abstract = {Abstract Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolithophore genus Gephyrocapsa with genomic analyses of extant species to assess the genetic processes underlying Pleistocene palaeontological patterns. We demonstrate that all modern diversity in Gephyrocapsa (including Emiliania huxleyi ) originated in a rapid species radiation during the last 0.6 Ma, coincident with the latest of the three pulses of Gephyrocapsa diversification and extinction documented in the fossil record. Our evolutionary genetic analyses indicate that new species in this genus have formed in sympatry or parapatry, with occasional hybridisation between species. This sheds light on the mode of speciation during evolutionary radiation of marine phytoplankton and provides a model of how new plankton species form.},
	keywords = {RCC1253, RCC1296, RCC3370, RCC3711, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034},
	issn = {2041-1723},
	doi = {10.1038/s41467-019-12169-7},
	url = {https://www.nature.com/articles/s41467-019-12169-7},
	author = {Bendif, El Mahdi and Nevado, Bruno and Wong, Edgar L. Y. and Hagino, Kyoko and Probert, Ian and Young, Jeremy R. and Rickaby, Rosalind E. M. and Filatov, Dmitry A.}
}
@article {Bendif2016,
	title = {Recent reticulate evolution in the ecologically dominant lineage of coccolithophores},
	journal = {Frontiers in Microbiology},
	volume = {7},
	number = {May},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC4032,RCC4033,RCC4034,RCC4035,RCC4036,rcc,sbr?hyto},
	month = {may},
	keywords = {2016, coccolithophores, cyto-nuclear discordance, diversity, Emiliania, evolution, Gephyrocapsa, introgressive hybridization, rcc, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, Reticulofenestra, sbr?hyto},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2016.00784},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.00784 http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00784/abstract},
	author = {Bendif, El Mahdi and Probert, Ian and D{\'\i}az-Rosas, Francisco and Thomas, Daniela and van den Engh, Ger and Young, Jeremy R. and von Dassow, Peter}
}
@article {Bendif2015,
	title = {Morphological and phylogenetic characterization of new gephyrocapsa isolates suggests introgressive hybridization in the Emiliania/Gephyrocapsa complex (haptophyta)},
	journal = {Protist},
	volume = {166},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: 2015,RCC1281,RCC1282,RCC1284,RCC1286,RCC1292,RCC1300,RCC1305,RCC1307,RCC1316,RCC1317,RCC1318,RCC1319,RCC1320,RCC1562,RCC1839,RCC3370,RCC3862,RCC3898,rcc},
	pages = {323{\textendash}336},
	abstract = {The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the No{\"e}laerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.},
	keywords = {2015, coccolithophores, Emiliania huxleyi, Gephyrocapsa muellerae, Gephyrocapsa oceanica, hybridization, phylogeny., rcc, RCC1281, RCC1282, RCC1284, RCC1286, RCC1292, RCC1300, RCC1305, RCC1307, RCC1316, RCC1317, RCC1318, RCC1319, RCC1320, RCC1562, RCC1839, RCC3370, RCC3862, RCC3898, species concept},
	issn = {14344610},
	doi = {10.1016/j.protis.2015.05.003},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461015000243},
	author = {Bendif, El Mahdi and Probert, Ian and Young, Jeremy R. and von Dassow, Peter}
}
@article {Decelle2015,
	title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy},
	journal = {Molecular Ecology Resources},
	volume = {15},
	number = {6},
	year = {2015},
	note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {1435{\textendash}1445},
	abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.},
	keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1755098X},
	doi = {10.1111/1755-0998.12401},
	url = {http://doi.wiley.com/10.1111/1755-0998.12401},
	author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard}
}
@article {Bendif2014,
	title = {Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)},
	journal = {Journal of Phycology},
	volume = {50},
	year = {2014},
	note = {tex.mendeley-tags: 2014,cc3549,rcc,rcc1210,rcc1213,rcc1220,rcc1227,rcc1229,rcc1242,rcc1252,rcc1253,rcc1258,rcc1259,rcc1260,rcc1271,rcc1281,rcc1288,rcc1292,rcc1297,rcc1300,rcc1303,rcc1305,rcc1316,rcc1562,rcc174,rcc1839,rcc3545,rrcc1247,sbr?hyto?ppo},
	pages = {140{\textendash}148},
	keywords = {2014, cc3549, rcc, rcc1210, RCC1213, rcc1220, rcc1227, rcc1229, RCC1242, rcc1252, RCC1253, rcc1258, RCC1259, rcc1260, rcc1271, RCC1281, rcc1288, RCC1292, rcc1297, RCC1300, RCC1303, RCC1305, RCC1316, RCC1562, rcc174, RCC1839, rcc3545, rrcc1247, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/jpy.12147},
	author = {Bendif, El Mahdi and Probert, Ian and Carmichael, Margaux and Romac, Sarah and Hagino, Kyoko and de Vargas, Colomban}
}
@article {Bendif2013,
	title = {On the description of Tisochrysis lutea gen . nov . sp . nov . and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta)},
	journal = {Journal of Applied Phycology},
	volume = {25},
	year = {2013},
	note = {tex.mendeley-tags: 2013,RCC1195,RCC1207,RCC1281,RCC1286,RCC1344,RCC1346,RCC1347,RCC1348,RCC1349,RCC1350,RCC1353,RCC2477,RCC3681,RCC3684,RCC3686,RCC3687,RCC3690,RCC3691,RCC3692,RCC3693,RCC3694,RCC3695,RCC3696,RCC3699,RCC3701,RCC3707,rcc,sbr?hyto?ppo},
	pages = {1763{\textendash}1776},
	keywords = {2013, dicrateria, imantonia, isochrysidaceae, isochrysis galbana, phylogeny, rcc, RCC1195, RCC1207, RCC1281, RCC1286, RCC1344, RCC1346, RCC1347, RCC1348, RCC1349, RCC1350, RCC1353, RCC2477, RCC3681, RCC3684, RCC3686, RCC3687, RCC3690, RCC3691, RCC3692, RCC3693, RCC3694, RCC3695, RCC3696, RCC3699, RCC3701, RCC3707, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, taxonomy, ultrastructure},
	doi = {10.1007/s10811-013-0037-0},
	author = {Bendif, El Mahdi and Probert, Ian and Schroeder, Declan C and de Vargas, Colomban}
}
@article {Jeanthon2011,
	title = {Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea},
	journal = {Biogeosciences},
	volume = {8},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {1955{\textendash}1970},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.5194/bg-8-1955-2011},
	author = {Jeanthon, Christian and Boeuf, Dominique and Dahan, Oc{\'e}ane and Le Gall, F and Garczarek, Laurence and Bendif, El Mahdi and Lehours, Anne-Catherine}
}
@article {Hagino2011,
	title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes},
	journal = {Journal of Phycology},
	volume = {47},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {1164{\textendash}1176},
	abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1529-8817.2011.01053.x},
	author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H}
}
