DNA-based species delimitation in algae

References

• Adams, N.G., Trainer, V.L., Rocap, G., Herwig, R.P. & Hauser, L. (2009). Genetic population structure of Pseudo-nitzschia pungens (Bacillariophyceae) from the Pacific Northwest and the North Sea. Journal of Phycology, 45: 1037–1045.
   PubMed Web of Science ®Google Scholar
• Álvarez, I. & Wendel, J.F. (2003). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29: 417–434.
   PubMed Web of Science ®Google Scholar
• Alverson, A.J. (2008). Molecular systematics and the diatom species. Protist, 159: 339–353.
   PubMed Web of Science ®Google Scholar
• Amato, A., Kooistra, W., Ghiron, J.H.L., Mann, D.G., Proschold, T. & Montresor, M. (2007). Reproductive isolation among sympatric cryptic species in marine diatoms. Protist, 158: 193–207.
   PubMed Web of Science ®Google Scholar
• Avise, J. (2000). Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, MA.
   Google Scholar
• Avise, J.C. & Ball, R.M. (1990). Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology, 7: 45–67.
   PubMed Web of Science ®Google Scholar
• Avise, J.C. & Wollenberg, K. (1997). Phylogenetics and the origin of species. Proceedings of the National Academy of Sciences USA, 94: 7748–7755.
   PubMed Web of Science ®Google Scholar
• Baird, N.A., Etter, P.D., Atwood, T.S., Currey, M.C., Shiver, A.L., Lewis, Z.A., Selker, E.U., Cresko, W.A. & Johnson, E.A. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3: e3376.
   PubMed Web of Science ®Google Scholar
• Barraclough, T.G. (2010). Evolving entities: towards a unified framework for understanding diversity at the species and higher levels. Philosophical Transactions of the Royal Society B – Biological Sciences, 365: 1801–1813.
   PubMed Web of Science ®Google Scholar
• Barrett, C.F. & Freudenstein, J.V. (2011). An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Molecular Ecology, 20: 2771–2786.
   PubMed Web of Science ®Google Scholar
• Baum, D.A. & Shaw, K.L. (1995). Genealogical perspectives on the species problem. In Experimental and Molecular Approaches to Plant Biosystematics (53) (Hoch, P.C. & Stephenson, A.G., editors), 289–303. Monographs in Systematic Botany from the Missouri Botanical Garden, St. Louis, MO.
   Google Scholar
• Baum, D.A. & Smith, S.D. (2012). Tree Thinking: An Introduction to Phylogenetic Biology. Roberts and Co., Greenwood Village, CO.
   Google Scholar
• Bendif, E.M., Probert, I., Herve, A., Billard, C., Goux, D., Lelong, C., Cadoret, J.-P. & Veron, B. (2011). Integrative taxonomy of the Pavlovophyceae (Haptophyta): a reassessment. Protist, 162: 738–761.
   PubMed Web of Science ®Google Scholar
• Bergsten, J., Bilton, D.T., Fujisawa, T., Elliott, M., Monaghan, M.T., Balke, M., Hendrich, L., Geijer, J., Herrmann, J., Foster, G.N., Ribera, I., Nilsson, A.N., Barraclough, T.G. & Vogler, A.P. (2012). The effect of geographical scale of sampling on DNA barcoding. Systematic Biology, 61: 851–869.
   PubMed Web of Science ®Google Scholar
• Birky, C.W., Jr. (2013). Species detection and identification in sexual organisms using population genetic theory and DNA sequences. PLoS One, 8: e52544.
   PubMed Web of Science ®Google Scholar
• Bittner, L., Halary, S., Payri, C., Cruaud, C., de Reviers, B., Lopez, P. & Bapteste, E. (2010). Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biology Direct, 5: 47.
   PubMed Web of Science ®Google Scholar
• Bittner, L., Gobet, A., Audic, S., Romac, S., Egge, E.S., Santini, S., Ogata, H., Probert, I., Edvardsen, B. & de Vargas, C. (2013). Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Molecular Ecology, 22: 87–101.
   PubMed Web of Science ®Google Scholar
• Boo, S.M., Kim, H.S., Shin, W., Boo, G.H., Cho, S.M., Jo, B.Y., Kim, J.H., Yang, E.C., Siver, P.A., Wolfe, A.P., Bhattacharya, D., Andersen, R.A. & Yoon, H.S. (2010). Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes. Molecular Ecology, 19: 4328–4338.
   PubMed Web of Science ®Google Scholar
• Brodie, J., Guiry, M.D. & Masuda, M. (1993). Life history, morphology and crossability of Chondrus ocellatus forma ocellatus and C. ocellatus forma crispoides (Gigartinales, Rhodophyta) from the north-western Pacific. European Journal of Phycology, 28: 183–196.
   Web of Science ®Google Scholar
• Brodie, J., Hayes, P.K., Barker, G.L. & Irvine, L.M. (1996). Molecular and morphological characters distinguishing two Porphyra species (Rhodophyta: Bangiophycidae). European Journal of Phycology, 31: 303–308.
   Web of Science ®Google Scholar
• Brown, S.D.J., Collins, R.A., Boyer, S., Lefort, M.-C., Malumbres-Olarte, J., Vink, C.J. & Cruickshank, R.H. (2012). Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources, 12: 562–565.
   PubMed Web of Science ®Google Scholar
• Caisová, L., Marin, B. & Melkonian, M. (2011). A close-up view on ITS2 evolution and speciation – a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evolutionary Biology, 11: 262.
   PubMed Web of Science ®Google Scholar
• Caisová, L., Marin, B. & Melkonian, M. (2013). A consensus secondary structure of ITS2 in the Chlorophyta identified by phylogenetic reconstruction. Protist, 164: 482–496.
   PubMed Web of Science ®Google Scholar
• Camargo, A. & Sites, J.J. (2013). Species delimitation: a decade after the renaissance. In The Species Problem – Ongoing Issues (Pavlinov, I., editor), 225–247. InTech, New York, NY.
   Google Scholar
• Camargo, A., Morando, M., Avila, L.J. & Sites, J.W., Jr. (2012). Species delimitation with ABC and other coalescent-based methods: A test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution, 66: 2834–2849.
   PubMed Web of Science ®Google Scholar
• Canovas, F.G., Mota, C.F., Serrao, E.A. & Pearson, G.A. (2011). Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation. BMC Evolutionary Biology, 11: 371.
   PubMed Web of Science ®Google Scholar
• Carstens, B.C. & Dewey, T.A. (2010). Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Systematic Biology, 59: 400–414.
   PubMed Web of Science ®Google Scholar
• Carstens, B.C., Pelletier, T.A., Reid, N.M. & Satler, J.D. (2013). How to fail at species delimitation. Molecular Ecology, 22: 4369–4383.
   PubMed Web of Science ®Google Scholar
• Casteleyn, G., Chepurnov, V.A., Leliaert, F., Mann, D.G., Bates, S.S., Lundholm, N., Rhodes, L., Sabbe, K. & Vyverman, W. (2008). Pseudo-nitzschia pungens (Bacillariophyceae): A cosmopolitan diatom species? Harmful Algae, 7: 241–257.
   Web of Science ®Google Scholar
• Casteleyn, G., Adams, N.G., Vanormelingen, P., Debeer, A.E., Sabbe, K. & Vyverman, W. (2009). Natural hybrids in the marine diatom Pseudo-nitzschia pungens (Bacillariophyceae): genetic and morphological evidence. Protist, 160: 343–354.
   PubMed Web of Science ®Google Scholar
• Casteleyn, G., Leliaert, F., Backeljau, T., Debeer, A.-E., Kotaki, Y., Rhodes, L., Lundholm, N., Sabbe, K. & Vyverman, W. (2010). Limits to gene flow in a cosmopolitan marine planktonic diatom. Proceedings of the National Academy of Sciences USA, 107: 12952–12957.
   PubMed Web of Science ®Google Scholar
• Coleman, A.W. (1977). Sexual and genetic isolation in cosmopolitan algal species Pandorina morum. American Journal of Botany, 64: 361–368.
   Web of Science ®Google Scholar
• Coleman, A.W. (2009). Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution, 50: 197–203.
   PubMed Web of Science ®Google Scholar
• Collins, R.A. & Cruickshank, R.H. (2013). The seven deadly sins of DNA barcoding. Molecular Ecology Resources, 13: 969–975.
   PubMed Web of Science ®Google Scholar
• Correa, A. & Baker, A. (2009). Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus Symbiodinium. Coral Reefs, 28: 81–93.
   Google Scholar
• Coyer, J.A., Peters, A.F., Hoarau, G., Stam, W.T. & Olsen, J.L. (2002). Hybridization of the marine seaweeds, Fucus serratus and Fucus evanescens (Heterokontophyta: Phaeophyceae) in a 100-year-old zone of secondary contact. Proceedings of the Royal Society B–Biological Sciences, 269: 1829–1834.
   PubMed Web of Science ®Google Scholar
• Coyer, J.A., Hoarau, G., Oudot-Le Secq, M.P., Stam, W.T. & Olsen, J.L. (2006). A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta). Molecular Phylogenetics and Evolution, 39: 209–222.
   PubMed Web of Science ®Google Scholar
• Coyne, J.A. & Orr, H.A. (2004). Speciation. Sinauer Associates, Sunderland, MA.
   Google Scholar
• Davis, J.I. & Nixon, K.C. (1992). Populations, genetic-variation, and the delimitation of phylogenetic species. Systematic Biology, 41: 421–435.
   Web of Science ®Google Scholar
• De Clerck, O., Gavio, B., Fredericq, S., Barbara, I. & Coppejans, E. (2005). Systematics of Grateloupia filicina (Halymeniaceae, Rhodophyta), based on rbcL sequence analyses and morphological evidence, including the reinstatement of G. minima and the description of G. capensis sp. nov. Journal of Phycology, 41: 391–410.
   Web of Science ®Google Scholar
• De Clerck, O., Guiry, M.D., Leliaert, F., Samyn, Y. & Verbruggen, H. (2013). Algal taxonomy: a road to nowhere? Journal of Phycology, 49: 215–225.
   PubMed Web of Science ®Google Scholar
• Degerlund, M., Huseby, S., Zingone, A., Sarno, D. & Landfald, B. (2012). Functional diversity in cryptic species of Chaetoceros socialis Lauder (Bacillariophyceae). Journal of Plankton Research, 34: 416–431.
   Web of Science ®Google Scholar
• Degnan, J.H. & Rosenberg, N.A. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution, 24: 332–340.
   PubMed Web of Science ®Google Scholar
• Demura, M., Noel, M.-H., Kasai, F., Watanabe, M.M. & Kawachi, M. (2009). Taxonomic revision of Chattonella antiqua, C. marina and C. ovata (Raphidophyceae) based on their morphological characteristics and genetic diversity. Phycologia, 48: 518–535.
   Web of Science ®Google Scholar
• De Queiroz, K. (2005). Ernst Mayr and the modern concept of species. Proceedings of the National Academy of Sciences USA, 102: 6600–6607.
   PubMed Web of Science ®Google Scholar
• De Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology, 56: 879–886.
   PubMed Web of Science ®Google Scholar
• de Senerpont Domis, L.N., Fama, P., Bartlett, A.J., Prud’homme van Reine, W.F. & Espinosa, C.A. (2003). Defining taxon boundaries in members of the morphologically and genetically plastic genus Caulerpa (Caulerpales, Chlorophyta). Journal of Phycology, 39: 1019–1037.
   Web of Science ®Google Scholar
• Destombe, C., Valero, M. & Guillemin, M.L. (2010). Delineation of two sibling red algal species, Gracilaria gracilis and Gracilaria dura (Gracilariales, Rhodophyta), using multiple DNA markers: resurrection of the species G. dura previously described in the Northern Atlantic 200 years ago. Journal of Phycology, 46: 720–727.
   Web of Science ®Google Scholar
• Dettman, J.R., Jacobson, D.J. & Taylor, J.W. (2003). A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution, 57: 2703–2720.
   PubMed Web of Science ®Google Scholar
• de Vargas, C., Norris, R., Zaninetti, L., Gibb, S.W. & Pawlowski, J. (1999). Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proceedings of the National Academy of Sciences USA, 96: 2864–2868.
   PubMed Web of Science ®Google Scholar
• de Vargas, C., Sáez, A.G., Medlin, L.K. & Thierstein, H.R. (2004). Super-species in the calcareous plankton. In Coccolithophores: From Molecular Processes to Global Impact (Thierstein, H.R. & Young, J.R., editors), 271–298. Springer-Verlag, Berlin.
   Google Scholar
• Dupuis, J.R., Roe, A.D. & Sperling, F.A.H. (2012). Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Molecular Ecology, 21: 4422–4436.
   PubMed Web of Science ®Google Scholar
• Edvardsen, B., Eikrem, W., Throndsen, J., Saez, A.G., Probert, I. & Medlin, L.K. (2011). Ribosomal DNA phylogenies and a morphological revision provide the basis for a revised taxonomy of the Prymnesiales (Haptophyta). European Journal of Phycology, 46: 202–228.
   Web of Science ®Google Scholar
• Emerson, K.J., Merz, C.R., Catchen, J.M., Hohenlohe, P.A., Cresko, W.A., Bradshaw, W.E. & Holzapfel, C.M. (2010). Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences USA, 107: 16196–16200.
   PubMed Web of Science ®Google Scholar
• Ence, D.D. & Carstens, B.C. (2011). SpedeSTEM: a rapid and accurate method for species delimitation. Molecular Ecology Resources, 11: 473–480.
   PubMed Web of Science ®Google Scholar
• Evans, K.M., Wortley, A.H. & Mann, D.G. (2007). An assessment of potential diatom barcode genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist, 158: 349–364.
   PubMed Web of Science ®Google Scholar
• Fraser, C.I., Hay, C.H., Spencer, H.G. & Waters, J.M. (2009). Genetic and morphological analyses of the southern bull kelp Durvillaea antarctica (Phaeophyceae: Durvillaeales) in New Zealand reveal cryptic species. Journal of Phycology, 45: 436–443.
   PubMed Web of Science ®Google Scholar
• Fraser, C.I., Winter, D.J., Spencer, H.G. & Waters, J.M. (2010). Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales). Molecular Phylogenetics and Evolution, 57: 1301–1311.
   PubMed Web of Science ®Google Scholar
• Freshwater, D.W., Tudor, K., O’Shaughnessy, K. & Wysor, B. (2010). DNA barcoding in the red algal order Gelidiales: comparison of COI with rbcL and verification of the “barcoding gap”. Cryptogamie Algologie, 31: 435–449.
   Web of Science ®Google Scholar
• Fucikova, K., Rada, J.C., Lukesova, A. & Lewis, L.A. (2011). Cryptic diversity within the genus Pseudomuriella Hanagata (Chlorophyta, Chlorophyceae, Sphaeropleales) assessed using four barcode markers. Nova Hedwigia, 93: 29–46.
   Web of Science ®Google Scholar
• Fujisawa, T. & Barraclough, T.G. (2014). Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: a revised method and evaluation on simulated datasets. Systematic Biology, 62: 707–724.
   Web of Science ®Google Scholar
• Fujita, M.K., Leaché, A.D., Burbrink, F.T., McGuire, J.A. & Moritz, C. (2012). Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology and Evolution, 27: 480–488.
   PubMed Web of Science ®Google Scholar
• Gile, G.H., Stern, R.F., James, E.R. & Keeling, P.J. (2010). DNA barcoding of Chlorarachniophytes using nucleomorph ITS sequences. Journal of Phycology, 46: 743–750.
   Web of Science ®Google Scholar
• Guiry, M.D. (1992). Species concepts in marine red algae. Progress in Phycological Research, 8: 251–278.
   Google Scholar
• Gutner-Hoch, E. & Fine, M. (2011). Genotypic diversity and distribution of Ostreobium quekettii within scleractinian corals. Coral Reefs, 30: 643–650.
   Web of Science ®Google Scholar
• Hagino, K., Bendif, E.M., Young, J.R., Kogame, K., Probert, I., Takano, Y., Horiguchi, T., de Vargas, C. & Okada, H. (2011). New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliania huxleyi (Prymnesiophyceae) from the cox1b-atp4 genes. Journal of Phycology, 47: 1164–1176.
   PubMed Web of Science ®Google Scholar
• Hall, J.D., Fucikova, K., Lo, C., Lewis, L.A. & Karol, K.G. (2010). An assessment of proposed DNA barcodes in freshwater green algae. Cryptogamie Algologie, 31: 529–555.
   Web of Science ®Google Scholar
• Hamsher, S.E., Evans, K.M., Mann, D.G., Poulickova, A. & Saunders, G.W. (2011). Barcoding diatoms: exploring alternatives to COI-5P. Protist, 162: 405–422.
   PubMed Web of Science ®Google Scholar
• Hare, M.P. (2001). Prospects for nuclear gene phylogeography. Trends in Ecology and Evolution, 16: 700–706.
   Web of Science ®Google Scholar
• Harrington, R.C. & Near, T.J. (2012). Phylogenetic and coalescent strategies of species delimitation in Snubnose Darters (Percidae: Etheostoma). Systematic Biology, 61: 63–79.
   PubMed Web of Science ®Google Scholar
• Hart, M.W. & Sunday, J. (2007). Things fall apart: biological species form unconnected parsimony networks. Biology Letters, 3: 509–512.
   PubMed Web of Science ®Google Scholar
• Hausdorf, B. (2011). Progress toward a general species concept. Evolution, 65: 923–931.
   PubMed Web of Science ®Google Scholar
• Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B–Biological Sciences, 270: 313–321.
   PubMed Web of Science ®Google Scholar
• Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S. & Francis, C.M. (2004). Identification of birds through DNA barcodes. PLoS Biology, 2: e312.
   PubMed Web of Science ®Google Scholar
• Hey, J. (2006). On the failure of modern species concepts. Trends in Ecology and Evolution, 21: 447–450.
   PubMed Web of Science ®Google Scholar
• Hey, J. & Pinho, C. (2012). Population genetics and objectivity in species diagnosis. Evolution, 66: 1413–1429.
   PubMed Web of Science ®Google Scholar
• Hickerson, M.J., Meyer, C.P. & Moritz, C. (2006). DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biology, 55: 729–739.
   PubMed Web of Science ®Google Scholar
• Hind, K.R. & Saunders, G.W. (2013). Molecular markers from three organellar genomes unravel complex taxonomic relationships within the coralline algal genus Chiharaea (Corallinales, Rhodophyta). Molecular Phylogenetics and Evolution, 67: 529–540.
   PubMed Web of Science ®Google Scholar
• Hiraoka, M., Ichihara, K., Zhu, W., Ma, J. & Shimada, S. (2011). Culture and hybridization experiments on an Ulva clade including the Qingdao strain blooming in the Yellow Sea. PLoS One, 6: e19371.
   PubMed Web of Science ®Google Scholar
• Hoef-Emden, K. (2007). Revision of the genus Cryptomonas (Cryptophyceae) II: incongruences between the classical morphospecies concept and molecular phylogeny in smaller pyrenoid-less cells. Phycologia, 46: 402–428.
   Web of Science ®Google Scholar
• Hoef-Emden, K. (2012). Pitfalls of establishing DNA barcoding systems in protists: the Cryptophyceae as a test case. PLoS One, 7: e43652.
   PubMed Web of Science ®Google Scholar
• Hovmoeller, R., Knowles, L.L. & Kubatko, L.S. (2013). Effects of missing data on species tree estimation under the coalescent. Molecular Phylogenetics and Evolution, 69: 1057–1062.
   PubMed Web of Science ®Google Scholar
• Hudson, R.R. & Coyne, J.A. (2002). Mathematical consequences of the genealogical species concept. Evolution, 56: 1557–1565.
   PubMed Web of Science ®Google Scholar
• Janouškovec, J., Liu, S.-L., Martone, P.T., Carré, W., Leblanc, C., Collén, J. & Keeling, P.J. (2013). Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One, 8: e59001.
   PubMed Web of Science ®Google Scholar
• John, D.M. & Maggs, C.A. (1997). Species problems in eukaryotic algae: a modern perspective. In Species: The Units of Biodiversity (Claridge, M.F., Dawah, H.A. & Wilson, M.R., editors), 83–107. Chapman & Hall, London.
   Google Scholar
• Kamiya, M. (2004). Speciation and biogeography of the Caloglossa leprieurii complex (Delesseriaceae, Rhodophyta). Journal of Plant Research, 117: 421–428.
   PubMed Web of Science ®Google Scholar
• Kermarrec, L., Franc, A., Rimet, F., Chaumeil, P., Humbert, J.F. & Bouchez, A. (2013). Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Molecular Ecology Resources, 13: 607–619.
   PubMed Web of Science ®Google Scholar
• Kim, J.I., Shin, W. & Triemer, R.E. (2013). Cryptic speciation in the genus Cryptoglena (Euglenaceae) revealed by nuclear and plastid SSU and LSU rRNA gene. Journal of Phycology, 49: 92–102.
   Web of Science ®Google Scholar
• Kizirian, D. & Donnelly, M. (2004). The criterion of reciprocal monophyly and classification of nested diversity at the species level. Molecular Phylogenetics and Evolution, 32: 1072–1076.
   PubMed Web of Science ®Google Scholar
• Klein, J., Sato, A., Nagl, S. & O’Huigín, C. (1998). Molecular trans-species polymorphism. Annual Review of Ecology and Systematics, 29: 1–21.
   Google Scholar
• Klopper, S., John, U., Zingone, A., Mangoni, O., Kooistra, W. & Cembella, A.D. (2013). Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? European Journal of Phycology, 48: 79–92.
   Web of Science ®Google Scholar
• Knowles, L.L. & Carstens, B.C. (2007). Delimiting species without monophyletic gene trees. Systematic Biology, 56: 887–895.
   PubMed Web of Science ®Google Scholar
• Krienitz, L. & Bock, C. (2012). Present state of the systematics of planktonic coccoid green algae of inland waters. Hydrobiologia, 698: 295–326.
   Web of Science ®Google Scholar
• Kucera, H. & Saunders, G.W. (2008). Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding. Botany, 86: 1065–1079.
   Web of Science ®Google Scholar
• Kucera, H. & Saunders, G.W. (2012). A survey of Bangiales (Rhodophyta) based on multiple molecular markers reveals cryptic diversity. Journal of Phycology, 48: 869–882.
   PubMed Web of Science ®Google Scholar
• Kusber, W.-H. & Jahn, R. (2003). Annotated list of diatom names by Horst Lange-Bertalot and co-workers. Version 3.0. www.algaterra.org/names_version3_0.pdf (accessed 13 Feb 2014).
   Google Scholar
• Kynčlová, A., Škaloud, P. & Škaloudová, M. (2010). Unveiling hidden diversity in the Synura petersenii species complex (Synurophyceae, Heterokontophyta). Nova Hedwigia Beiheft, 136: 283–298.
   Web of Science ®Google Scholar
• LaJeunesse, T.C. & Thornhill, D.J. (2011). Improved resolution of reef-coral endosymbiont (Symbiodinium) species diversity, ecology, and evolution through psbA non-coding region genotyping. PLoS One, 6: e29013.
   PubMed Web of Science ®Google Scholar
• LaJeunesse, T.C., Parkinson, J.E. & Reimer, J.D. (2012). A genetics-based description of Symbiodinium minutum sp. nov. and S. psygmophilum sp. nov. (Dinophyceae), two dinoflagellates symbiotic with cnidaria. Journal of Phycology, 48: 1380–1391.
   Web of Science ®Google Scholar
• Lam, D.W., Entwisle, T.J., Eloranta, P., Kwandrans, J. & Vis, M.L. (2012). Circumscription of species in the genus Sirodotia (Batrachospermales, Rhodophyta) based on molecular and morphological data. European Journal of Phycology, 47: 42–50.
   Web of Science ®Google Scholar
• Lane, C.E., Lindstrom, S.C. & Saunders, G.W. (2007). A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding. Molecular Phylogenetics and Evolution, 44: 634–648.
   PubMed Web of Science ®Google Scholar
• Lange, M., Chen, Y.Q. & Medlin, L.K. (2002). Molecular genetic delineation of Phaeocystis species (Prymnesiophyceae) using coding and non-coding regions of nuclear and plastid genomes. European Journal of Phycology, 37: 77–92.
   Web of Science ®Google Scholar
• Le Gall, L. & Saunders, G.W. (2010). DNA barcoding is a powerful tool to uncover algal diversity: a case study of the Phyllophoraceae (Gigartinales, Rhodophyta) in the Canadian flora. Journal of Phycology, 46: 374–389.
   Web of Science ®Google Scholar
• Leaché, A.D. & Fujita, M.K. (2010). Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society B–Biological Sciences, 277: 3071–3077.
   PubMed Web of Science ®Google Scholar
• Leaché, A.D., Harris, R.B., Rannala, B. & Yang, Z. (2014). The influence of gene flow on species tree estimation: a simulation study. Systematic Biology, 63: 17–30.
   PubMed Web of Science ®Google Scholar
• Leavitt, S.D., Fankhauser, J.D., Leavitt, D.H., Porter, L.D., Johnson, L.A. & St. Clair, L.L. (2011). Complex patterns of speciation in cosmopolitan ‘‘rock posy’’ lichens – discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Molecular Phylogenetics and Evolution, 59: 587–602.
   PubMed Web of Science ®Google Scholar
• Leliaert, F., Verbruggen, H., Wysor, B. & De Clerck, O. (2009). DNA taxonomy in morphologically plastic taxa: algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales). Molecular Phylogenetics and Evolution, 53: 122–133.
   PubMed Web of Science ®Google Scholar
• Lelong, A., Hegaret, H., Soudant, P. & Bates, S.S. (2012). Pseudo-nitzschia (Bacillariophyceae) species, domoic acid and amnesic shellfish poisoning: revisiting previous paradigms. Phycologia, 51: 168–216.
   Web of Science ®Google Scholar
• Lemmon, A.R., Emme, S.A. & Lemmon, E.M. (2012). Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, 61: 727–744.
   PubMed Web of Science ®Google Scholar
• Lin, S., Zhang, H., Hou, Y., Zhuang, Y. & Miranda, L. (2009). High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob genes for dinoflagellate DNA barcoding. Applied and Environmental Microbiology, 75: 1279–1290.
   PubMed Web of Science ®Google Scholar
• Litaker, R.W., Vandersea, M.W., Kibler, S.R., Reece, K.S., Stokes, N.A., Lutzoni, F.M., Yonish, B.A., West, M.A., Black, M.N.D. & Tester, P.A. (2007). Recognizing dinoflagellate species using ITS rDNA sequences. Journal of Phycology, 43: 344–355.
   Web of Science ®Google Scholar
• Litaker, R.W., Vandersea, M.W., Faust, M.A., Kibler, S.R., Chinain, M., Holmes, M.J., Holland, W.C. & Tester, P.A. (2009). Taxonomy of Gambierdiscus including four new species, Gambierdiscus caribaeus, Gambierdiscus carolinianus, Gambierdiscus carpenteri and Gambierdiscus ruetzleri (Gonyaulacales, Dinophyceae). Phycologia, 48: 344–390.
   Web of Science ®Google Scholar
• Liu, H., Probert, I., Uitz, J., Claustre, H., Aris-Brosou, S., Frada, M., Not, F. & de Vargas, C. (2009). Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proceedings of the National Academy of Sciences USA, 106: 12803–12808.
   PubMed Web of Science ®Google Scholar
• Logares, R., Rengefors, K., Kremp, A., Shalchian-Tabrizi, K., Boltovskoy, A., Tengs, T., Shurtleff, A. & Klaveness, D. (2007). Phenotypically different microalgal morphospecies with identical ribosomal DNA: a case of rapid adaptive evolution? Microbial Ecology, 53: 549–561.
   PubMed Web of Science ®Google Scholar
• Lundholm, N., Moestrup, O., Kotaki, Y., Hoef-Emden, K., Scholin, C. & Miller, P. (2006). Inter- and intraspecific variation of the Pseudo-nitzschia delicatissima complex (Bacillariophyceae) illustrated by rRNA probes, morphological data and phylogenetic analyses. Journal of Phycology, 42: 464–481.
   Web of Science ®Google Scholar
• Lundholm, N., Bates, S.S., Baugh, K.A., Bill, B.D., Connell, L.B., Léger, C. & Trainer, V.L. (2012). Cryptic and pseudo-cryptic diversity in diatoms – with descriptions of Pseudo-nitzschia hasleana sp. nov. and P. fryxelliana sp. nov. Journal of Phycology, 48: 436–454.
   PubMed Web of Science ®Google Scholar
• Luo, W., Proschold, T., Bock, C. & Krienitz, L. (2010). Generic concept in Chlorella-related coccoid green algae (Chlorophyta, Trebouxiophyceae). Plant Biology, 12: 545–553.
   PubMed Web of Science ®Google Scholar
• Lurling, M. (2003). Phenotypic plasticity in the green algae Desmodesmus and Scenedesmus with special reference to the induction of defensive morphology. Annales de Limnologie, 39: 85–101.
   Web of Science ®Google Scholar
• Macaya, E.C. & Zuccarello, G.C. (2010). DNA barcoding and genetic divergence in the giant kelp macrocystis (Laminariales). Journal of Phycology, 46: 736–742.
   Web of Science ®Google Scholar
• Maddison, W.P. (1997). Gene trees in species trees. Systematic Biology, 46: 523–536.
   Web of Science ®Google Scholar
• Maddison, W.P. & Knowles, L.L. (2006). Inferring phylogeny despite incomplete lineage sorting. Systematic Biology, 55: 21–30.
   PubMed Web of Science ®Google Scholar
• Maggs, C.A., Fletcher, H.L., Fewer, D., Loade, L., Mineur, F. & Johnson, M.P. (2011). Speciation in red algae: members of the Ceramiales as model organisms. Integrative and Comparative Biology, 51: 492–504.
   PubMed Web of Science ®Google Scholar
• Mailund, T. (2009). On gene trees and species trees. Available at http://www.mailund.dk/index.php/2009/02/12/on-gene-trees-and-species-trees/ (last accessed 22 Jan 2014).
   Google Scholar
• Mallet, J. (1995). A species definition for the modern synthesis. Trends in Ecology and Evolution, 10: 294–299.
   PubMed Web of Science ®Google Scholar
• Manhart, J.R. & McCourt, R.M. (1992). Molecular data and species concepts in the algae. Journal of Phycology, 28: 730–737.
   Web of Science ®Google Scholar
• Mann, D.G. (1999). The species concept in diatoms. Phycologia, 38: 437–495.
   Web of Science ®Google Scholar
• Mann, D.G. (2010). Discovering diatom species: is a long history of disagreements about species-level taxonomy now at an end? Plant Ecology and Evolution, 143: 251–264.
   Web of Science ®Google Scholar
• Mann, D.G., Sato, S., Trobajo, R., Vanormelingen, P. & Souffreau, C. (2010). DNA barcoding for species identification and discovery in diatoms. Cryptogamie Algologie, 31: 557–577.
   Web of Science ®Google Scholar
• Masters, B.C., Fan, V. & Ross, H.A. (2011). Species delimitation – a geneious plugin for the exploration of species boundaries. Molecular Ecology Resources, 11: 154–157.
   PubMed Web of Science ®Google Scholar
• Mattio, L. & Payri, C. (2010). Assessment of five markers as potential barcodes for identifying Sargassum subgenus Sargassum species (Phaeophyceae, Fucales). Cryptogamie Algologie, 31: 467–485.
   Web of Science ®Google Scholar
• Mayden, R.L. (1997). A hierarchy of species concepts: the denouement in the saga of the species problem. In Species: The Units of Biodiversity (Claridge, M.F., Dawah, H.A. & Wilson, M.R., editors), 381–424. Chapman and Hall, London.
   Google Scholar
• Mayr, E. (1996). What is a species, and what is not? Philosophy of Science, 63: 262–277.
   Web of Science ®Google Scholar
• Mayr, E. & Ashlock, P.D. (1991). Principles of Systematic Zoology. McGraw-Hill, New York, NY.
   Google Scholar
• McCormack, J.E., Maley, J.M., Hird, S.M., Derryberry, E.P., Graves, G.R. & Brumfield, R.T. (2012). Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution, 62: 397–406.
   PubMed Web of Science ®Google Scholar
• McCormack, J.E., Hird, S.M., Zellmer, A.J., Carstens, B.C. & Brumfield, R.T. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66: 526–538.
   PubMed Web of Science ®Google Scholar
• McDevit, D.C. & Saunders, G.W. (2009). On the utility of DNA barcoding for species differentiation among brown macroalgae (Phaeophyceae) including a novel extraction protocol. Phycological Research, 57: 131–141.
   Web of Science ®Google Scholar
• McManus, H.A. & Lewis, L.A. (2011). Molecular phylogenetic relationships in the freshwater family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), with an emphasis on Pediastrum duplex. Journal of Phycology, 47: 152–163.
   PubMed Web of Science ®Google Scholar
• Meier, R., Shiyang, K., Vaidya, G. & Ng, P.K.L. (2006). DNA barcoding and taxonomy in diptera: a tale of high intraspecific variability and low identification success. Systematic Biology, 55: 715–728.
   PubMed Web of Science ®Google Scholar
• Meyer, C.P. & Paulay, G. (2005). DNA barcoding: error rates based on comprehensive sampling. PLoS Biology, 3: 2229–2238.
   Web of Science ®Google Scholar
• Milstein, D. & Saunders, G.W. (2012). DNA barcoding of Canadian Ahnfeltiales (Rhodophyta) reveals a new species – Ahnfeltia borealis sp. nov. Phycologia, 51: 247–259.
   Web of Science ®Google Scholar
• Mols-Mortensen, A., Neefus, C.D., Nielsen, R., Gunnarsson, K., Egilsdóttir, S., Pedersen, P.M. & Brodie, J. (2012). New insights into the biodiversity and generic relationships of foliose Bangiales (Rhodophyta) in Iceland and the Faroe Islands. European Journal of Phycology, 47: 146–159.
   Web of Science ®Google Scholar
• Monaghan, M.T., Wild, R., Elliot, M., Fujisawa, T., Balke, M., Inward, D.J., Lees, D.C., Ranaivosolo, R., Eggleton, P., Barraclough, T.G. & Vogler, A.P. (2009). Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology, 58: 298–311.
   PubMed Web of Science ®Google Scholar
• Moniz, M.B.J. & Kaczmarska, I. (2010). Barcoding of diatoms: nuclear encoded ITS revisited. Protist, 161: 7–34.
   PubMed Web of Science ®Google Scholar
• Moniz, M.B.J., Rindi, F., Novis, P.M., Broady, P.A. & Guiry, M.D. (2012). Molecular phylogeny of Antarctic Prasiola (Prasiolales, Trebouxiophyceae) reveals extensive cryptic diversity. Journal of Phycology, 48: 940–955.
   PubMed Web of Science ®Google Scholar
• Moon-van der Staay, S.Y., De Wachter, R. & Vaulot, D. (2001). Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature, 409: 607–610.
   PubMed Web of Science ®Google Scholar
• Müller, T., Philippi, N., Dandekar, T., Schultz, J. & Wolf, M. (2007). Distinguishing species. RNA, 13: 1469–1472.
   PubMed Web of Science ®Google Scholar
• Neustupa, J., Šťastný, J., Nemjová, K., Mazalová, P., Goodyer, E., Poulíčková, A. & Škaloud, P. (2011). A novel, combined approach to assessing species delimitation and biogeography within the well-known desmid species Micrasterias fimbriata and M. rotata (Desmidiales, Steptophyta). Hydrobiologia, 667: 223–239.
   Web of Science ®Google Scholar
• Ni-Ni-Win, Hanyuda, T., Draisma, S.G.A., Furnari, G., Meinesz, A. & Kawai, H. (2011). Padina ditristromatica sp. nov. and Padina pavonicoides sp. nov. (Dictyotales, Phaeophyceae), two new species from the Mediterranean Sea based on morphological and molecular markers. European Journal of Phycology, 46: 327–341.
   Web of Science ®Google Scholar
• Niemiller, M.L., Near, T.J. & Fitzpatrick, B.M. (2012). Delimiting species using multilocus data: diagnosing cryptic diversity in the Southern Cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution, 66: 846–866.
   PubMed Web of Science ®Google Scholar
• Niwa, K., Iida, S., Kato, A., Kawai, H., Kikuchi, N., Kobiyama, A. & Aruga, Y. (2009). Genetic diversity and introgression in two cultivated species (Porphyra yezoensis and Porphyra tenera) and closely related wild species of Porphyra (Bangiales, Rhodophyta). Journal of Phycology, 45: 493–502.
   PubMed Web of Science ®Google Scholar
• Nosil, P., Funk, D.J. & Ortiz-Barrientos, D. (2009). Divergent selection and heterogeneous genomic divergence. Molecular Ecology, 18: 375–402.
   PubMed Web of Science ®Google Scholar
• Not, F., Siano, R., Kooistra, W.H.C.F., Simon, N., Vaulot, D. & Probert, I. (2012). Diversity and ecology of eukaryotic marine phytoplankton. Advances in Botanical Research, 64: 1–53.
   Web of Science ®Google Scholar
• O’Meara, B.C. (2010). New heuristic methods for joint species delimitation and species tree inference. Systematic Biology, 59: 59–73.
   PubMed Web of Science ®Google Scholar
• Palumbi, S.R., Cipriano, F. & Hare, M.P. (2001). Predicting nuclear gene coalescence from mitochondrial data: the three-times rule. Evolution, 55: 859–868.
   Web of Science ®Google Scholar
• Pamilo, P. & Nei, M. (1988). Relationships between gene trees and species trees. Molecular Biology and Evolution, 5: 568–583.
   PubMed Web of Science ®Google Scholar
• Pawlowski, J. & Holzmann, M. (2009). Diversity and geographic distribution of benthic foraminifera: a molecular perspective. In Protist Diversity and Geographical Distribution (8) (Foissner, W. & Hawksworth, D., editors), 83–94. Springer, the Netherlands.
   Google Scholar
• Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., Bowser, S.S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A.M., Gile, G.H., Holzmann, M., Jahn, R., Jirku, M., Keeling, P.J., Kostka, M., Kudryavtsev, A., Lara, E., Lukes, J., Mann, D.G., Mitchell, E.A.D., Nitsche, F., Romeralo, M., Saunders, G.W., Simpson, A.G.B., Smirnov, A.V., Spouge, J.L., Stern, R.F., Stoeck, T., Zimmermann, J., Schindel, D. & de Vargas, C. (2012). CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biology, 10: e1001419.
   PubMed Web of Science ®Google Scholar
• Payo, D.A., Leliaert, F., Verbruggen, H., D’Hondt, S., Calumpong, H.P. & De Clerck, O. (2013). Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines. Proceedings of the Royal Society B–Biological Sciences, 280: 20122660.
   PubMed Web of Science ®Google Scholar
• Peters, A.F., Van Wijk, S.J., Cho, G.Y., Scornet, D., Hanyuda, T., Kawai, H., Schroeder, D.C., Cock, J.M. & Boo, S.M. (2010). Reinstatement of Ectocarpus crouaniorum Thuret in Le Jolis as a third common species of Ectocarpus (Ectocarpales, Phaeophyceae) in Western Europe, and its phenology at Roscoff, Brittany. Phycological Research, 58: 157–170.
   Web of Science ®Google Scholar
• Piganeau, G., Eyre-Walker, A., Grimsley, N. & Moreau, H. (2011). How and why DNA barcodes underestimate the diversity of microbial eukaryotes. PLoS One, 6: e16342.
   PubMed Web of Science ®Google Scholar
• Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D. & Vogler, A.P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55: 595–609.
   PubMed Web of Science ®Google Scholar
• Posada, D. & Crandall, K.A. (2001). Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution, 16: 37–45.
   PubMed Web of Science ®Google Scholar
• Powell, J.R. (2012). Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data. Methods in Ecology and Evolution, 3: 1–11.
   Web of Science ®Google Scholar
• Pröschold, T., Marin, B., Schlosser, U.G. & Melkonian, M. (2001). Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist, 152: 265–300.
   PubMed Web of Science ®Google Scholar
• Pröschold, T., Darienko, T., Silva, P.C., Reisser, W. & Krienitz, L. (2011). The systematics of Zoochlorella revisited employing an integrative approach. Environmental Microbiology, 13: 350–364.
   PubMed Web of Science ®Google Scholar
• Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. (2011). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, 21: 1864–1877.
   PubMed Web of Science ®Google Scholar
• Reid, N. & Carstens, B. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology, 12: 196.
   PubMed Web of Science ®Google Scholar
• Rindi, F., Mikhailyuk, T.I., Sluiman, H.J., Friedl, T. & López-Bautista, J.M. (2011). Phylogenetic relationships in Interfilum and Klebsormidium (Klebsormidiophyceae, Streptophyta). Molecular Phylogenetics and Evolution, 58: 218–231.
   PubMed Web of Science ®Google Scholar
• Robba, L., Russell, S.J., Barker, G.L. & Brodie, J. (2006). Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). American Journal of Botany, 93: 1101–1108.
   PubMed Web of Science ®Google Scholar
• Roe, A.D., Rice, A.V., Bromilow, S.E., Cooke, J.E.K. & Sperling, F.A.H. (2010). Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle. Molecular Ecology Resources, 10: 946–959.
   PubMed Web of Science ®Google Scholar
• Rosenberg, N.A. & Nordborg, M. (2002). Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics, 3: 380–390.
   PubMed Web of Science ®Google Scholar
• Rybalka, N., Andersen, R.A., Kostikov, I., Mohr, K.I., Massalski, A., Olech, M. & Friedl, T. (2009). Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae). Environmental Microbiology, 11: 554–565.
   PubMed Web of Science ®Google Scholar
• Rybalka, N., Wolf, M., Andersen, R. & Friedl, T. (2013). Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae). BMC Evolutionary Biology, 13: 39.
   PubMed Web of Science ®Google Scholar
• Saez, A.G., Probert, I., Geisen, M., Quinn, P., Young, J.R. & Medlin, L.K. (2003). Pseudo-cryptic speciation in coccolithophores. Proceedings of the National Academy of Sciences USA, 100: 7163–7168.
   PubMed Web of Science ®Google Scholar
• Sampayo, E.M., Dove, S. & Lajeunesse, T.C. (2009). Cohesive molecular genetic data delineate species diversity in the dinoflagellate genus Symbiodinium. Molecular Ecology, 18: 500–519.
   PubMed Web of Science ®Google Scholar
• Sato, S., Nishimura, T., Uehara, K., Sakanari, H., Tawong, W., Hariganeya, N., Smith, K., Rhodes, L., Yasumoto, T., Taira, Y., Suda, S., Yamaguchi, H. & Adachi, M. (2011). Phylogeography of Ostreopsis along West Pacific coast, with special reference to a novel clade from Japan. PLoS One, 6: e27983.
   PubMed Web of Science ®Google Scholar
• Saunders, G.W. (2005). Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philosophical Transactions of the Royal Society B–Biological Sciences, 360: 1879–1888.
   PubMed Web of Science ®Google Scholar
• Saunders, G.W. & Kucera, H. (2010). An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae. Cryptogamie Algologie, 31: 487–528.
   Web of Science ®Google Scholar
• Saunders, G.W. & McDevit, D.C. (2012). Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms. Methods in Molecular Biology, 858: 207–222.
   PubMedGoogle Scholar
• Schmidt, M., Horn, S., Flieger, K., Ehlers, K., Wilhelm, C. & Schnetter, R. (2012). Synchroma pusillum sp. nov. and other new algal isolates with chloroplast complexes confirm the Synchromophyceae (Ochrophyta) as a widely distributed group of amoeboid algae. Protist, 163: 544–559.
   PubMed Web of Science ®Google Scholar
• Serrao, E.A., Alice, L.A. & Brawley, S.H. (1999). Evolution of the Fucaceae (Phaeophyceae) inferred from nrDNA-ITS. Journal of Phycology, 35: 382–394.
   Web of Science ®Google Scholar
• Shaffer, H.B. & Thomson, R.C. (2007). Delimiting species in recent radiations. Systematic Biology, 56: 896–906.
   PubMed Web of Science ®Google Scholar
• Shaw, K.L. (1998). Species and the diversity of natural groups. In Endless Forms: Species and Speciation (Howard, D.J. & Berlocher, S.H., editors), 44–56. Oxford University Press, Oxford.
   Google Scholar
• Sherwood, A.R. & Presting, G.G. (2007). Universal primers amplify a 23S rDNA plastid marker in eukaryotic algae and cyanobacteria. Journal of Phycology, 43: 605–608.
   Web of Science ®Google Scholar
• Sherwood, A.R., Vis, M.L., Entwisle, T.J., Necchi Jr, O. & Presting, G.G. (2008). Contrasting intra versus interspecies DNA sequence variation for representatives of the Batrachospermales (Rhodophyta): insights from a DNA barcoding approach. Phycological Research, 56: 269–279.
   Web of Science ®Google Scholar
• Sherwood, A.R., Sauvage, T., Kurihara, A., Conklin, K.Y. & Presting, G.G. (2010). A comparative analysis of COI, LSU and UPA marker data for the Hawaiian florideophyte Rhodophyta: implications for DNA barcoding of red algae. Cryptogamie Algologie, 31: 451–465.
   Web of Science ®Google Scholar
• Silberfeld, T., Bittner, L., Fernández-García, C., Cruaud, C., Rousseau, F., de Reviers, B., Leliaert, F., Payri, C.E. & De Clerck, O. (2013). Species diversity, phylogeny and large scale biogeographic patterns of the genus Padina (Phaeophyceae, Dictyotales). Journal of Phycology, 49: 130–142.
   PubMed Web of Science ®Google Scholar
• Simpson, G.G. (1951). The species concept. Evolution and Development, 5: 285–298.
   Web of Science ®Google Scholar
• Sites, J.W. & Marshall, J.C. (2003). Delimiting species: a Renaissance issue in systematic biology. Trends in Ecology and Evolution, 18: 462–470.
   Web of Science ®Google Scholar
• Škaloud, P. & Peksa, O. (2010). Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta). Molecular Phylogenetics and Evolution, 54: 36–46.
   PubMed Web of Science ®Google Scholar
• Škaloud, P. & Rindi, F. (2013). Ecological differentiation of cryptic species within an asexual protist morphospecies: a case study of filamentous green alga Klebsormidium (Streptophyta). Journal of Eukaryotic Microbiology, 60: 350–362.
   PubMed Web of Science ®Google Scholar
• Škaloud, P., Kynclova, A., Benada, O., Kofronova, O. & Skaloudova, M. (2012). Toward a revision of the genus Synura, section Petersenianae (Synurophyceae, Heterokontophyta): morphological characterization of six pseudo-cryptic species. Phycologia, 51: 303–329.
   Web of Science ®Google Scholar
• Šlapeta, J., Lopez-Garcia, P. & Moreira, D. (2006). Global dispersal and ancient cryptic species in the smallest marine eukaryotes. Molecular Biology and Evolution, 23: 23–29.
   PubMed Web of Science ®Google Scholar
• Soehner, S., Zinssmeister, C., Kirsch, M. & Gottschling, M. (2012). Who am I – and if so, how many? Species diversity of calcareous dinophytes (Thoracosphaeraceae, Peridiniales) in the Mediterranean Sea. Organisms Diversity and Evolution, 12: 339–348.
   Google Scholar
• Souffreau, C., Vanormelingen, P., Van de Vijver, B., Isheva, T., Verleyen, E., Sabbe, K. & Vyverman, W. (2013). Molecular evidence for distinct Antarctic lineages in the cosmopolitan terrestrial diatoms Pinnularia borealis and Hantzschia amphioxys. Protist, 164: 101–115.
   PubMed Web of Science ®Google Scholar
• Stern, R.F., Horak, A., Andrew, R.L., Coffroth, M.-A., Andersen, R.A., Küpper, F.C., Jameson, I., Hoppenrath, M., Véron, B., Kasai, F., Brand, J., James, E.R. & Keeling, P.J. (2010). Environmental barcoding reveals massive dinoflagellate diversity in marine environments. PLoS One, 5: e13991.
   PubMed Web of Science ®Google Scholar
• Stern, R.F., Andersen, R.A., Jameson, I., Küpper, F.C., Coffroth, M.-A., Vaulot, D., Le Gall, F., Véron, B., Brand, J.J., Skelton, H., Kasai, F., Lilly, E.L. & Keeling, P.J. (2012). Evaluating the ribosomal Internal Transcribed Spacer (ITS) as a candidate dinoflagellate barcode marker. PLoS One, 7: e42780.
   PubMed Web of Science ®Google Scholar
• Subirana, L., Péquin, B., Michely, S., Escande, M.-L., Meilland, J., Derelle, E., Marin, B., Piganeau, G., Desdevises, Y., Moreau, H. & Grimsley, N.H. (2013). Morphology, genome plasticity, and phylogeny in the genus Ostreococcus reveal a cryptic species, O. mediterraneus sp. nov. (Mamiellales, Mamiellophyceae). Protist, 164: 643–659.
   PubMed Web of Science ®Google Scholar
• Sutherland, J.E., Lindstrom, S.C., Nelson, W.A., Brodie, J., Lynch, M.D.J., Hwang, M.S., Choi, H.-G., Miyata, M., Kikuchi, N., Oliveira, M.C., Farr, T., Neefus, C., Mols-Mortensen, A., Milstein, D. & Müller, K.M. (2011). A new look at an ancient order: generic revision of the Bangiales (Rhodophyta). Journal of Phycology, 47: 1131–1151.
   PubMed Web of Science ®Google Scholar
• Sym, S.D., Pienaar, R.N., Edvardsen, B. & Egge, E.S. (2011). Fine structure and systematics of Prymnesium radiatum sp. nov. (Prymnesiophyceae) from False Bay and Franskraal, South Africa. European Journal of Phycology, 46: 229–248.
   Web of Science ®Google Scholar
• Tautz, D., Arctander, P., Minelli, A., Thomas, R.H. & Vogler, A.P. (2003). A plea for DNA taxonomy. Trends in Ecology and Evolution, 18: 70–74.
   Web of Science ®Google Scholar
• Taylor, J.W., Jacobson, D.J., Kroken, S., Kasuga, T., Geiser, D.M., Hibbett, D.S. & Fisher, M.C. (2000). Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, 31: 21–32.
   PubMed Web of Science ®Google Scholar
• Templeton, A.R. (2001). Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology, 10: 779–791.
   PubMed Web of Science ®Google Scholar
• Templeton, A.R., Crandall, K.A. & Sing, C.F. (1992). A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA-sequence data. 3. Cladogram estimation. Genetics, 132: 619–633.
   PubMed Web of Science ®Google Scholar
• Trainor, F.R. (1998). Biological aspects of Scenedesmus (Chlorophyceae) phenotypic plasticity. Nova Hedwigia Beiheft, 117: 1–367.
   Google Scholar
• Tronholm, A., Steen, F., Tyberghein, L., Leliaert, F., Verbruggen, H., Siguan, M.A.R. & De Clerck, O. (2010). Species delimitation, taxonomy, and biogeography of Dictyota in Europe (Dictyotales, Phaeophyceae). Journal of Phycology, 46: 1301–1321.
   Web of Science ®Google Scholar
• Tronholm, A., Leliaert, F., Sanson, M., Afonso-Carrillo, J., Tyberghein, L., Verbruggen, H. & De Clerck, O. (2012). Contrasting geographical distributions as a result of thermal tolerance and long-distance dispersal in two allegedly widespread tropical brown algae. PLoS One, 7: e30813.
   PubMed Web of Science ®Google Scholar
• van der Strate, H.J., Boele-Bos, S.A., Olsen, J.L., van de Zande, L. & Stam, W.T. (2002). Phylogeographic studies in the tropical seaweed Cladophoropsis membranacea (Chlorophyta, Ulvophyceae) reveal a cryptic species complex. Journal of Phycology, 38: 572–582.
   Web of Science ®Google Scholar
• Vanelslander, B., Créach, V., Vanormelingen, P., Ernst, A., Chepurnov, V.A., Sahan, E., Muyzer, G., Stal, L.J., Vyverman, W. & Sabbe, K. (2009). Ecological differentiation between sympatric pseudocryptic species in the estuarine benthic diatom Navicula phyllepta (Bacillariophyceae). Journal of Phycology, 45: 1278–1289.
   PubMed Web of Science ®Google Scholar
• Vanormelingen, P., Hegewald, E., Braband, A., Kitschke, M., Friedl, T., Sabbe, K. & Vyverman, W. (2007). The systematics of a small spineless Desmodesmus species, D. constato-granulatus (Sphaeropleales, Chlorophyceae), based on ITS2 rDNA sequence analyses and cell wall morphology. Journal of Phycology, 43: 378–396.
   Web of Science ®Google Scholar
• Vanormelingen, P., Chepurnov, V.A., Mann, D.G., Sabbe, K. & Vyverman, W. (2008). Genetic divergence and reproductive barriers among morphologically heterogeneous sympatric clones of Eunotia bilunaris sensu lato (Bacillariophyta). Protist, 159: 73–90.
   PubMed Web of Science ®Google Scholar
• Verbruggen, H. (2014). Morphological complexity, plasticity, and species diagnosability in the application of old species names in DNA-based taxonomies. Journal of Phycology, 50: 26–31.
   Google Scholar
• Verbruggen, H., Leliaert, F., Maggs, C.A., Shimada, S., Schils, T., Provan, J., Booth, D., Murphy, S., De Clerck, O., Littler, D.S., Littler, M.M. & Coppejans, E. (2007). Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences. Molecular Phylogenetics and Evolution, 44: 240–254.
   PubMed Web of Science ®Google Scholar
• Verbruggen, H., Vlaeminck, C., Sauvage, T., Sherwood, A.R., Leliaert, F. & De Clerck, O. (2009). Phylogenetic analysis of Pseudochlorodesmis strains reveals cryptic diversity above the family level in the siphonous green algae (Bryopsidales, Chlorophyta). Journal of Phycology, 45: 726–731.
   Web of Science ®Google Scholar
• Wagner, C.E., Keller, I., Wittwer, S., Selz, O.M., Mwaiko, S., Greuter, L., Sivasundar, A. & Seehausen, O. (2013). Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22: 787–798.
   PubMed Web of Science ®Google Scholar
• Walker, R.H., Brodie, J., Russell, S., Irvine, L.M. & Orfanidis, S. (2009). Biodiversity of coralline algae in the northeastern Atlantic including Corallina caespitosa sp. nov. (Corallinoideae, Rhodophyta). Journal of Phycology, 45: 287–297.
   PubMed Web of Science ®Google Scholar
• Wiens, J.J. (2007). Species delimitation: new approaches for discovering diversity. Systematic Biology, 56: 875–878.
   PubMed Web of Science ®Google Scholar
• Wiens, J.J. & Penkrot, T.A. (2002). Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology, 51: 69–91.
   PubMed Web of Science ®Google Scholar
• Wiley, E.O. (1978). The Evolutionary Species Concept reconsidered. Systematic Zoology, 21: 17–26.
   Google Scholar
• Wilkins, J.S. (2009). Species: A History of the Idea. University of California Press, Berkeley, CA.
   Google Scholar
• Wolf, M., Chen, S., Song, J., Ankenbrand, M. & Müller, T. (2013). Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences – a proof of concept. PLoS One, 8: e66726.
   PubMed Web of Science ®Google Scholar
• Yang, Z. & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences USA, 107: 9264–9269.
   PubMed Web of Science ®Google Scholar
• Zachos, F.E. & Lovari, S. (2013). Taxonomic inflation and the poverty of the Phylogenetic Species Concept – a reply to Gippoliti and Groves. Hystrix - Italian Journal of Mammalogy, 24: 142–144.
   Google Scholar
• Zardi, G.I., Nicastro, K.R., Canovas, F., Ferreira Costa, J., Serrão, E.A. & Pearson, G.A. (2011). Adaptive traits are maintained on steep selective gradients despite gene flow and hybridization in the intertidal zone. PLoS One, 6: e19402.
   PubMed Web of Science ®Google Scholar
• Zimmermann, J., Jahn, R. & Gemeinholzer, B. (2011). Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Organisms Diversity and Evolution, 11: 173–192.
   Google Scholar
• Zink, R.M. & Barrowclough, G.F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17: 2107–2121.
   PubMed Web of Science ®Google Scholar
• Zuccarello, G.C. & Lokhorst, G.M. (2005). Molecular phylogeny of the genus Tribonema (Xanthophyceae) using rbcL gene sequence data: monophyly of morphologically simple algal species. Phycologia, 44: 384–392.
   Web of Science ®Google Scholar
• Zuccarello, G.C. & West, J.A. (2003). Multiple cryptic species: molecular diversity and reproductive isolation in the Bostrychia radicans/B. moritziana complex (Rhodomelaceae, Rhodophyta) with focus on North American isolates. Journal of Phycology, 39: 948–959.
   Web of Science ®Google Scholar
• Zuccarello, G.C., Schidlo, N., McIvor, L. & Guiry, M.D. (2005). A molecular re-examination of speciation in the intertidal red alga Mastocarpus stellatus (Gigartinales, Rhodophyta) in Europe. European Journal of Phycology, 40: 337–344.
   Web of Science ®Google Scholar