We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used to illustrate the points are derived from marine photosynthetic eukaryotic protists. It has been accepted that we know less than 10% of the identified diversity in the marine microbial world and the marine micro- and pico-eukaryotes are no exception. Even the species that we think we can easily recognize are often poorly described, and even less is known of their life histories and spatial and temporal trends in their abundance and distribution. With new molecular and analytical techniques, we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. Biogeochemical reactions performed by marine photosynthetic microbial organisms constitute a major sustaining component of ecosystem functioning, and therefore, affect climate changes. New interpretations of how environmental, ecological and evolutionary processes control and structure marine ecosystem biodiversity can be made so that we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study without good analytical methods.

Medlin L.K. 2011. The Permian–Triassic mass extinction forces the radiation of the modern marine phytoplankton. Phycologia 50: 684–693. DOI: 10.2216/10-31.1 Among modern eukaryotic marine phytoplanktonic lineages possessing red algal plastids are the diatoms, dinoflagellates and haptophytes including coccolithophorids. Although origins of these host lineages and the timing of the endosymbioses leading to their ability to photosynthesize are ancient, their modern radiations are not. Molecular clocks suggest the timing of the origins and the radiations of these host lineages are different among the three groups. Dinoflagellates and haptophytes had class and order level radiations from 500 to 600 megaannum (Ma) and genus-level radiations, especially among the thecate dinoflagellates, about 250 Ma. Pigmented heterokonts, the last divergence in the heterokont tree, originated between 770 and 1000 Ma, but most planktonic unicellular groups diverged at the Permian–Triassic (P/T) boundary (250 Ma) and radiated th...

Williams and Kociolek ( 2007 Williams, DM and Kociolek, JP . 2007. The rejection of paraphyletic taxa. Eur. J. Phycol., 42: 313–319. [Taylor & Francis Online], [Web of Science ®] [Google Scholar] : Eur. J. Phycol., 42: 313–319) have presented an opinion paper in which they review some principles of classification and criticize the most recent classification of the diatoms by Medlin & Kaczmarska ( 2004 Medlin, LK and Kaczmarska, I . 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia, 43: 245–270. [Crossref], [Web of Science ®] [Google Scholar] : Phycologia, 43: 245–270). In their critique of paraphyletic groups, they failed to consider one paraphyletic relationship that is most frequently revealed by molecular data, which in part justifies the recognition of paraphyletic taxa among certain diatom genera. In their criticism of the most recent classification system of the diatoms, they have misinterpreted and misrepresented much of the molecular data that they have used as evidence against this classification system and thus have made incorrect comparisons among published phylogenies of the diatoms.