David G. Mann

The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

Abstract. This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional “kingdoms.” The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

3. Biodiversity, biogeography and conservation of diatoms

Recent morphometric and breeding studies of diatoms show that the present species classification is too coarse and hides significant diversity. Many species are subdivided into phenodemes, which often differ in cell size, shape, stria density and pattern, but may also have different ultrastructural features. In raphid diatoms these can include the form of the raphe endings, details of the pore occlusions, and the structure of the girdle, while chloroplast structure can also vary. The phenodemes can be sympatric or allopatric. In Sellaphora pupula and other species, sympatric phenodemes are reproductively isolated. It is recommended that such demes are recognized as separate species; the total number of diatom species worldwide may thus be at least 2 × 105. Use of a fine-grained classification reveals that many diatom species may be endemics, some restricted to a single lake or catchment, others to wider areas. Environmental impact assessments and conservation strategies must begin to take account of endemism and rarity among microscopic algae and protists.

Evolution of the diatoms: insights from fossil, biological and molecular data

P.A. Sims, D.G. Mann and L.K. Medlin. 2006. Evolution of the diatoms: insights from fossil, biological and molecular data.Phycologia 45: 361–402. DOI: 10.2216/05-22.1 Molecular sequence analyses have yielded many important insights into diatom evolution, but there have been few attempts to relate these to the extensive fossil record of diatoms, probably because of unfamiliarity with the data available, which are scattered widely through the geological literature. We review the main features of molecular phylogenies and concentrate on the correspondence between these and the fossil record; we also review the evolution of major morphological, cytological and life cycle characteristics, and possible diatom origins. The first physical remains of diatoms are from the Jurassic, and well-preserved, diverse floras are available from the Lower Cretaceous. Though these are unequivocally identifiable as centric diatoms, none except a possible Stephanopyxis can be unequivocally linked to lineages of extant diatoms, although it is almost certain that members of the Coscinodiscophyceae (radial centrics) and Mediophyceae (polar centrics) were present; some display curious morphological features that hint at an unorthodox cell division mechanism and life cycle. It seems most likely that the earliest diatoms were marine, but recently discovered fossil deposits hint that episodes of terrestrial colonization may have occurred in the Mesozoic, though the main invasion of freshwaters appears to have been delayed until the Cenozoic. By the Upper Cretaceous, many lineages are present that can be convincingly related to extant diatom taxa. Pennate diatoms appear in the late Cretaceous and raphid diatoms in the Palaeocene, though molecular phylogenies imply that raphid diatoms did in fact evolve considerably earlier. Recent evidence shows that diatoms are substantially underclassified at the species level, with many semicryptic or cryptic species to be recognized; however, there is little prospect of being able to discriminate between such taxa in fossil material.

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.

Historical processes constrain patterns in global diatom diversity

There is a long-standing belief that microbial organisms have unlimited dispersal capabilities, are therefore ubiquitous, and show weak or absent latitudinal diversity gradients. In contrast, using a global freshwater diatom data set, we show that latitudinal gradients in local and regional genus richness are present and highly asymmetric between both hemispheres. Patterns in regional richness are explained by the degree of isolation of lake districts, while the number of locally coexisting diatom genera is highly constrained by the size of the regional diatom pool, habitat availability, and the connectivity between habitats within lake districts. At regional to global scales, historical factors explain significantly more of the observed geographic patterns in genus richness than do contemporary environmental conditions. Together, these results stress the importance of dispersal and migration in structuring diatom communities at regional to global scales. Our results are consistent with predictions from the theory of island biogeography and metacommunity concepts and likely underlie the strong provinciality and endemism observed in the relatively isolated diatom floras in the Southern Hemisphere.

Experimental Studies on Sexual Reproduction in Diatoms

The diatoms are the most speciose group of algae, having global ecological significance in the carbon and silicon cycles. They are almost unique among algae in being diplontic, and sexual reproduction is an obligate stage in the life cycle of most diatom species. It is unclear which are the principal factors that have fostered the evolutionary success of diatoms, but the unique life cycle (which is correlated with a curious wall structure and cell division mechanism) and size-dependent control of sexuality must have played an important part. Progress in understanding life cycle dynamics and their interrelationships with population biology and evolution will depend on how successfully sex can be initiated and manipulated experimentally, and our review provides a foundation for such work. Relevant data are scattered in time and come mostly from non-English publications, producing a false impression of diatoms as recalcitrant with respect to sexualization. Recent advances dependent on experimental cultures include the discovery of widespread heterothallism (including some complex types of behavior) in pennate diatoms, sexual diversity among clones of centric diatoms, more flexible size restitution strategies in centric diatoms than had been suspected, and use of reproductive isolation as a criterion in diatom taxonomy. We identify unsolved problems in the life history of diatoms, including aspects of sexualization, cell-cell recognition, sexual reproduction, and the development of the special expanding cell (the auxospore), which is crucial to morphogenesis in this group. Some of these problems are being addressed using modern molecular genetic tools, and progress will be facilitated when whole-genome sequences are published (e.g., for Thalassiosira pseudonana). Problems of culture maintenance and methods for manipulating the life cycle are discussed.

Diversity, Nomenclature, and Taxonomy of Protists

the origin of echolocation and flight in bats. Nature 403:188– 192. van Rheede, T., T. Bastiaans, D. N. Boone, S. B. Hedges, W. W. de Jong, and O. Madsen. 2006. The platypus in its place: nuclear genes and indels confirm the sister group relation of monotremes and therians. Mol. Biol. Evol. 23:587–597. Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141– 154. Waddell, P. J., N. Okada, and M. Hasegawa. 1999. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48:1–5. Waddell, P. J., and S. Shelley. 2003. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ -fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28:197–224.

REPRODUCTIVE COMPATIBILITY AND rDNA SEQUENCE ANALYSES IN THE SELLAPHORA PUPULA SPECIES COMPLEX (BACILLARIOPHYTA) 1

We tested whether internal transcribed spacer (ITS) rDNA sequence differences are correlated with sexual compatibility in the Sellaphora pupula complex, a model system for investigations of the species concept and speciation in diatoms. The phylogenetic relationships among the demes and the systematic position of the genus within the raphid diatoms were also investigated. The division of clones of S. pupula and S. laevissima into groups, based on sequence similarities and phylogenetic analyses, resembled groupings based on sexual compatibility: A high ITS sequence divergence, making full alignment difficult or impossible, was found among clones whose gametangia do not interact, whereas there was little sequence divergence among interfertile clones. This is clearly consistent with the idea that “Z clades” exhibit less intraclade than interclade variation in ITS and, as comparisons of secondary structure models for the RECT and PSEUDOCAP clones showed, that there is an equivalence of “CBC” and Z clades in the rectangular and pseudocapitate demes of S. pupula, as earlier hypothesized for chlorophytes. Intraclonal, presumably intraindividual, variation in ITS was found in S. pupula, though with a degree of variation less than that found within a single Z clade; it was too minor to affect the interclonal relationships in the ITS phylogeny. Sellaphora, which appears monophyletic in 18S phylogenies, with Pinnularia and “Navicula”pelliculosa as its closest allies, may also include some species currently classified in Eolimna. The S. pupula–S. laevissima group began to diversify in or before the Miocene.

The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species

Abstract Morphometric shape analysis and ultrastructural data are provided for six genodemes of the Sellaphora pupula species complex that have been studied during the last 20 years from Blackford Pond, Edinburgh, UK. The demes have previously been shown to be separated by prezygotic reproductive barriers: cells of different demes do not pair, though they may show residual interactions when sexualized. A new morphometric method, contour segment analysis, which was recently developed for diatoms in relation to automated identification, gives a clear separation of all six genodemes and indicates no heterogeneity within each. Legendre shape analysis gives less separation in this instance. All other available data, including molecular sequence data, also support separation of the six demes at species level. Five new species are therefore described: S. auldreekie, S. blackfordensis, S. capitata, S. lanceolata and S. obesa. The identity of S. pupula sensu stricto is clarified through designation of epitypes.

An inordinate fondness? The number, distributions, and origins of diatom species.

The number of extant species of diatoms is estimated here to be at least 30,000 and probably ca. 100,000, by extrapolation from an eclectic sample of genera and species complexes. Available data, although few, indicate that the pseudocryptic species being discovered in many genera are not functionally equivalent. Molecular sequence data show that some diatom species are ubiquitously dispersed. A good case can be made that at least some diatom species and even a few genera are endemics, but many such claims are still weak. The combination of very large species numbers and relatively rapid dispersal in diatoms is inconsistent with some versions of the “ubiquity hypothesis” of protist biogeography, and appears paradoxical. However, population genetic data indicate geographical structure in all the (few) marine and freshwater species that have been examined in detail, sometimes over distances of a few tens of kilometres. The mode of speciation may often be parapatric, in the context of a constantly shifting mosaic of temporarily isolated (meta) populations, but if our “intermediate dispersal hypothesis” is true (that long‐distance dispersal is rare, but not extremely rare), allopatric speciation could also be maximized.