Search

Species- and genus-level taxonomy of desmids depends largely on shape and detail of the cell wall and chloroplast morphology. The depth of most desmid semicells, relative to the focal depth of conventional light microscopes, means that morphological characteristics are usually illustrated by drawings, made from material that is mounted in water to allow reorientation of specimens to different aspects of shape and pattern. Though a productive approach for two centuries, this has the disadvantages that features not initially detected or thought irrelevant are not recorded, drawing quality is variable, and individual specimens are rarely retained for further study. We describe methods for making permanent preparations of desmid cell walls and using these to produce extended depth of focus summary images and three-dimensional (3-D) reconstructions. Together with World-Wide Web dissemination of image stacks, these advances make it practical to make a desirable change from typification via drawings to typification via single or multiple preserved specimens. They will also facilitate standardization of taxon concepts and identification.

We describe tools for automatic identification and classification of diatoms that compare photographs with other photographs and drawings, via a model. Identification of diatoms, i.e. assigning a new specimen to one of the known species, has applications in many disciplines, including ecology, palaeoecology and forensic science. The model we build represents life cycle and natural variation of both shape and texture over multiple diatom species, derived automatically from photographs and/or drawings. The model can be used to automatically produce drawings of diatoms at any stage of their life cycle development. Similar drawings are traditionally used for diatom identification, and encapsulate visually salient diatom features. In this article, we describe the methods used for analysis of photographs and drawings, present our model of diatom shape and texture variation, and finish with results of identification experiments using photographs and drawings as well as a detailed evaluation.

An earlier study demonstrated the presence of 11 morphologically distinct demes (‘morphotypes’) within the Diploneis smithii/D. fusca species complex in a single sample from Ganavan near Oban on Sc...

A group of unusual Diploneis species has been examined using light and scanning electron microscopy. Diploneis sejuncta is peculiar in Diploneis because its longitudinal canals are separated from the raphe sternum furrows, whereas in most other species they are adjacent. Diploneis sejuncta f. constricta has also been examined and is elevated to specific rank as D. solea. A fossil member of the group, Navicula sejuncta var. baldjikiana from upper Miocene deposits from eastern Europe is intermediate in morphology between D. sejuncta and D. solea and is elevated to specific level as D. praesejuncta. Three other species related to D. sejuncta are described for the first time: D. pneumatica, D. biremijormis, and D. colae. All members of this group share a distinctive zig-zag arrangement of internal pores; the same arrangement is present in D. totarae, an upper Eocene diatom described from Oamaru, New Zealand, suggesting that this species lineage is at least 37 million years old. The implications of th...

Summary Morphological variation within the Diploneis smithii — D. fusca complex has been examined critically in a single collection from Oban, Scotland. Eleven distinct sympatric morphotypes can be identified. Each exhibits a recognizable size-reduction sequence in which all critical characters are stable. Measurements of dimensions, striation density and rectangularity are combined with two other characters (shape of central raphe endings and the arrangement of pores on the surface of the valves) in statistical analyses (including Principal Components Analysis and Hierarchical Clustering Analysis) that demonstrate objectively the validity of the groupings. The implications of such discontinuities are discussed with respect to current knowledge of patterns of reproduction in diatoms, breeding barriers between similar races, and phenotypic plasticity. The morphotypes probably represent taxa with different ecological preferences, and should in due course be given taxonomic recognition to avoid loss of information. Distinct morphotypes similar to those in D. smithii — D. fusca occur within the species of other genera, and the phenomenon may be very widespread among diatoms.

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.

This paper introduces the project ADIAC (Automatic Diatom Identification and Classification), which started in May 1998 and which is financed by the European MAST (Marine Science and Technology) programme. The main goal is to develop algorithms for an automatic identification of diatoms using image information: both valve shape (contour) and ornamentation. The paper presents the goals of the project as well as first results on shape modeling and contour extraction. Public data are available in order to create student projects beyond the ADIAC partnership.

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.

The Royal Botanic Garden Edinburgh and the Natural History Museum are collaborating to establish a database and linked iconograph, wherever possible using TDWG (Taxonomic Databases Working Group) standards, that can handle complex nomenclature; specimen information; specimen and population descriptions that can later be assembled automatically to generate taxon descriptions and also used as a basis for the automatic or semi-automatic generation of keys and on-line identification; original descriptions of taxa; bibliography; and images. The system is at present being developed using the PANDORA floristic database system (on an AREV base) and is being designed to be compatible with other database systems suitable for use in botanic gardens and herbaria.