Mayr E. Populations, species, and evolution: an abridgment of animal species and evolution. Cambridge: Belknap Press of Harvard University Press; 1970.
Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, et al. Cryptic species as a window on diversity and conservation. Trends Ecol Evol. 2007;22:148–55.
Fišer C, Robinson CT, Malard F. Cryptic species as a window into the paradigm shift of the species concept. Mol Ecol. 2018;27:613–35.
Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, et al. Finding evolutionary processes hidden in cryptic species. Trends Ecol Evol. 2018;33:153–63.
Sarno D, Kooistra WHCF, Medlin LK, Percopo I, Zingone A. Diversity in the genus Skeletonema (Bacillariophyceae). II. An assessment of the taxonomy of S. costatum-like species with the description of four new species. J Phycol. 2005;41:151–76.
Gaonkar CC, Kooistra WHCF, Lange CB, Montresor M, Sarno D. Two new species in the Chaetoceros socialis complex (Bacillariophyta): C. sporotruncatus and C. dichatoensis, and characterization of its relatives. J Phycol. 2017;53:889–907.
Li Y, Boonprakob A, Gaonkar CC, Kooistra WHCF, Lange CB, Hernández-Becerril D, et al. Diversity in the globally distributed diatom genus Chaetoceros (Bacillariophyceae): three new species from warm-temperate waters. PLoS ONE. 2017;12:e0168887.
Finlay BJ, Clarke KJ. Ubiquitous dispersal of microbial species. Nature. 1999;400:828.
Finlay BJ, Fenchel T. Divergent perspectives on protist species richness. Protist. 1999;150:229–33.
Fenchel T, Finlay BJ. The ubiquity of small species: patterns of local and global diversity. Bioscience. 2004;54:777.
Fenchel T. Cosmopolitan microbes and their ‘cryptic’ species. Aquat Microb Ecol. 2005;41:49–54.
Miglietta MP, Faucci A, Santini F. Speciation in the sea: overview of the symposium and discussion of future directions. Integr Comp Biol. 2011;51:449–55.
Kooistra WHCF, Sarno D, Balzano S, Gu H, Andersen RA, Zingone A. Global diversity and biogeography of Skeletonema species (Bacillariophyta). Protist. 2008;159:177–93.
Nanjappa D, Audic S, Romac S, Kooistra WHCF, Zingone A. Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach. PLoS ONE. 2014;9:e103810.
Kaczmarska I, Mather L, Luddington IA, Muise F, Ehrman JM. Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy. Am J Bot. 2014;101:267–86.
Zhao Y, Yi Z, Gentekaki E, Zhan A, Al-Farraj SA, Song W. Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists. Mol Phylogenet Evol. 2016;94:718–29.
Weiner A, Aurahs R, Kurasawa A, Kitazato H, Kucera M. Vertical niche partitioning between cryptic sibling species of a cosmopolitan marine planktonic protist. Mol Ecol. 2012;21:4063–73.
Lamari N, Ruggiero MV, d’Ippolito G, Kooistra WHCF, Fontana A, Montresor M. Specificity of lipoxygenase pathways supports species delineation in the marine diatom genus Pseudo-nitzschia. PLoS ONE. 2013;8:e73281.
Škaloud P, Friedl T, Hallmann C, Beck A, Dal Grande F. Taxonomic revision and species delimitation of coccoid green algae currently assigned to the genus Dictyochloropsis (Trebouxiophyceae, Chlorophyta). J Phycol. 2016;52:599–617.
de Jesus PB, Costa AL, de Castro Nunes JM, Manghisi A, Genovese G, Morabito M, et al. Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae, Rhodophyta). Eur J Phycol. 2019;54:135–53.
Díaz-Tapia P, Ly M, Verbruggen H. Extensive cryptic diversity in the widely distributed Polysiphonia scopulorum (Rhodomelaceae, Rhodophyta): molecular species delimitation and morphometric analyses. Mol Phylogenet Evol. 2020;152:106909.
Huson DH, Rupp R, Scornavacca C. Phylogenetic networks. Cambridge: Cambridge University Press; 2009.
Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254–67.
Solís-Lemus C, Yang M, Ané C. Inconsistency of species tree methods under gene flow. Syst Biol. 2016;65:843–51.
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, et al. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol. 2017;26:5872–95.
Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, et al. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 2012;10:e1001419.
Trobajo R, Mann DG, Clavero E, Evans KM, Vanormelingen P, McGregor RC. The use of partial cox1, rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschia palea species complex (Bacillariophyceae). Eur J Phycol. 2010;45:413–25.
Decelle J, Suzuki N, Mahé F, De Vargas C, Not F. Molecular phylogeny and morphological evolution of the acantharia (Radiolaria). Protist. 2012;163:435–50.
Stoeck T, Przybos E, Dunthorn M. The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates. Mol Ecol Resour. 2014;14:458–68.
Moniz MBJ, Kaczmarska I. Barcoding of diatoms: nuclear encoded ITS revisited. Protist. 2010;161:7–34.
Gile GH, Stern RF, James ER, Keeling PJ. DNA barcoding of chlorarachniophytes using nucleomorph ITS sequences. J Phycol. 2010;46:743–50.
Stern RF, Andersen RA, Jameson I, Küpper FC, Coffroth M-A, Vaulot D, et al. Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker. PLoS ONE. 2012;7:e42780.
Saunders GW. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc B Biol Sci. 2005;360:1879–88.
MacGillivary ML, Kaczmarska I. Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms. J Eukaryot Microbiol. 2011;58:529–36.
Zimmermann J, Jahn R, Gemeinholzer B. Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Org Divers Evol. 2011;11:173–92.
Piredda R, Tomasino MP, D’Erchia AM, Manzari C, Pesole G, Montresor M, et al. Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site. FEMS Microbiol Ecol. 2016;93:fiw200.
Pawlowski J, Lecroq B. Short rDNA barcodes for species identification in foraminifera. J Eukaryot Microbiol. 2010;57:197–205.
Mordret S, Piredda R, Vaulot D, Montresor M. Kooistra WHCF, Sarno D. dinoref: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol Ecol Resour. 2018;18:974–87.
Gaonkar CC, Piredda R, Minucci C, Mann DG, Montresor M, Sarno D, et al. Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae. PLoS ONE. 2018;13:e0208929.
Balzano S, Percopo I, Siano R, Gourvil P, Chanoine M, Marie D, et al. Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex. J Phycol. 2017;53:161–87.
Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, et al. The ocean sampling day consortium. Gigascience. 2015;4. https://doi.org/10.1186/s13742-015-0066-5.
Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, et al. Open science resources for the discovery and analysis of Tara Oceans data. Sci Data. 2015;2:150023.
Yau S, Lopes dos Santos A, Eikrem W, Gérikas Ribeiro C, Gourvil P, Balzano S, et al. Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic. J Phycol. 2020;56:37–51.
Lopes Dos Santos A, Gourvil P, Tragin M, Noël M-H, Decelle J, Romac S, et al. Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. ISME J. 2017;11:512–28.
Kuwata A, Yamada K, Ichinomiya M, Yoshikawa S, Tragin M, Vaulot D, et al. Bolidophyceae, a sister picoplanktonic group of diatoms—a review. Front Mar Sci. 2018;5:370.
Segawa T, Matsuzaki R, Takeuchi N, Akiyoshi A, Navarro F, Sugiyama S, et al. Bipolar dispersal of red-snow algae. Nat Commun. 2018;9:1–8.
Ichinomiya M, Dos Santos AL, Gourvil P, Yoshikawa S, Kamiya M, Ohki K, et al. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J. 2016;10:2419–34.
Tragin M, Vaulot D. Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding. Sci Rep. 2019;9:1–14.
Morard R, Vollmar NM, Greco M, Kucera M. Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species. PLoS ONE. 2019;14:e0213936.
Pinseel E, Janssens SB, Verleyen E, Vanormelingen P, Kohler TJ, Biersma EM, et al. Global radiation in a rare biosphere soil diatom. Nat Commun. 2020;11:1–12.
Hasle GR, Syvertsen EE. Marine diatoms. In: Tomas CR, editor. Identifying marine phytoplankton. San Diego: Academic Press; 1997. pp 5–385.
Kooistra WHCF, Sarno D, Hernández-Becerril DU, Assmy P, Di Prisco C, Montresor M. Comparative molecular and morphological phylogenetic analyses of taxa in the Chaetocerotaceae (Bacillariophyta). Phycologia. 2010;49:471–500.
De Luca D, Sarno D, Piredda R, Kooistra WHCF. A multigene phylogeny to infer the evolutionary history of Chaetocerotaceae (Bacillariophyta). Mol Phylogenet Evol. 2019;140:106575.
Longhurst AR. Toward and ecological geography of the sea. In: Longhurst AR, editor. Ecological geography of the sea. 2nd ed. Cambridge: Academic Press; 2007. pp 1–17.
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.
Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE. 2009;4:e6372.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
De Vargas C, Audic S, Tara Oceans Consortium C, Tara Oceans Expedition P. Total V9 rDNA information organized at the metabarcode level for the Tara Oceans Expedition (2009–12). 2017. PANGAEA. https://doi.org/10.1594/PANGAEA.873277.
Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, et al. Global trends in marine plankton diversity across kingdoms of life. Cell. 2019;179:1084–97.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160–6.
Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
Han MV, Zmasek CM. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinform. 2009;10:356.
Templeton AR, Crandall KA, Sing CF. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 1992;132:619–33.
Clement M, Posada D, Crandall KA. TCS: a computer program to estimate gene genealogies. Mol Ecol. 2000;9:1657–9.
Leigh JW, Bryant D. popart: full‐feature software for haplotype network construction. Methods Ecol Evol. 2015;6:1110–6.
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
Jukes TH, Cantor CR. Evolution of protein molecules. Mamm Protein Metab. 1969;3:21–132.
Meyer CP, Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 2005;3:e422.
R Core Team. R: a language and environment for statistical computing. 2019. Vienna, Austria: R Foundation for Statistical Computing; 2019.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2016. https://ggplot2.tidyverse.org.
Becker A, Wilks AR. Maps: draw geographical maps. 2018. https://CRAN.R-project.org/package=maps.
Markmann M, Tautz D. Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philos Trans R Soc Lond B Biol Sci. 2005;360:1917–24.
López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, Del Campo J. Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Sci Rep. 2018;8:9106.
Álvarez I, Wendel JF. Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol. 2003;29:417–34.
Alverson AJ, Kolnick L. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). J Phycol. 2005;41:1248–57.
Gaonkar CC, Piredda R, Sarno D, Zingone A, Montresor M, Kooistra WHCF. Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity. Environ Microbiol. 2020;22:1917–29.
Cleve PT. Pelagisk Diatomeer från Kattegat. In: Petersen CGJ, editor. Det Videnskabelige Udbytte af Kanonbaaden ‘Hauchs’ Togter i de Danske Have Indefor Skagen, I. Aarene 1883–86. Kjøbenhavn: Andr. Fred. Høst & Sons Forlag; 1889. pp 53–56.
Gran HH. Den Norske Nordhaus-Expedition 1876-1878. Botanik, Protophyta: Diatomaceae, Silicoflagellata og Cilioflagellata. Christiania: Grøndal & Søns; 1897.
De Luca D, Kooistra WHCF, Sarno D, Gaonkar CC, Piredda R. Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies. PeerJ. 2019;7:e7410.
Wang J, Wu J. Occurrence and potential risks of harmful algal blooms in the East China Sea. Sci Total Environ. 2009;407:4012–21.
Zhen Y, Mi T, Yu Z. Detection of several harmful algal species by sandwich hybridization integrated with a nuclease protection assay. Harmful Algae. 2009;8:651–7.
Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, et al. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. bioRxiv. 2019. https://doi.org/10.1101/867739.
Sarno D, Kooistra WHCF, Balzano S, Hargraves PE, Zingone A. Diversity in the genus Skeletonema (Bacillariophyceae). III. Phylogenetic position and morphological variability of Skeletonema costatum and Skeletonema grevillei, with the description of Skeletonema ardens sp. nov. J Phycol. 2007;43:156–70.
Hasle GR. The biogeography of some marine planktonic diatoms. Deep Sea Res Oceanogr Abstr. 1976;23:319–338, IN1-IN6.
Pargana A. Functional and molecular diversity of the diatom family Leptocylindraceae. 2017. PhD Thesis, The Open University, Milton Keynes, UK.
Novis PM. Taxonomy of Klebsormidium (Klebsormidiales, Charophyceae) in New Zealand streams and the significance of low-pH habitats. Phycologia. 2006;45:293–301.
Rindi F, Guiry MD, López-Bautista JM. Distribution, morphology, and phylogeny of Klebsormidium (Klebsormidiales, Charophyceae) in urban environments in Europe. J Phycol. 2008;44:1529–40.
Rindi F, Mikhailyuk TI, Sluiman HJ, Friedl T, López-Bautista JM. Phylogenetic relationships in Interfilum and Klebsormidium (Klebsormidiophyceae, Streptophyta). Mol Phylogenet Evol. 2011;58:218–31.
Škaloud P, Rindi F. Ecological differentiation of cryptic species within an asexual protist morphospecies: a case study of filamentous green alga Klebsormidium (Streptophyta). J Eukaryot Microbiol. 2013;60:350–62.
Baas Becking LGM. Geobiologie of Inleiding tot de Milieukunde. The Hague: Van Stockum & Zoon; 1934).
Shapiro BJ, Leducq J-B, Mallet J. What is speciation? PLoS Genet. 2016;12:e1005860.
Godhe A, Rynearson T. The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments. Philos Trans R Soc Lond B Biol Sci. 2017;372:20160399.
de Vargas C, Norris R, Zaninetti L, Gibb SW, Pawlowski J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc Natl Acad Sci USA. 1999;96:2864–8.
Amato A, Kooistra WHCF, Levialdi Ghiron JH, Mann DG, Pröschold T, Montresor M. Reproductive isolation among sympatric cryptic species in marine diatoms. Protist. 2007;158:193–207.
Weisse T. Distribution and diversity of aquatic protists: an evolutionary and ecological perspective. Biodivers Conserv. 2007;17:243–59.
Vanelslander B, Créach V, Vanormelingen P, Ernst A, Chepurnov VA, Sahan E, et al. Ecological differentiation between sympatric pseudocryptic species in the estuarine benthic diatom Navicula phyllepta (Bacillariophyceae). J Phycol. 2009;45:1278–89.
Source: Ecology - nature.com
