Our research programmes and their development
We have published on phenology, ferns and herbarium management, but we concentrate on algae, especially the largest group of algae, the diatoms. Our interests are broad and include cell biology, morphogenesis and ecology, but we publish mostly in the fields of systematics and evolution, taxonomy, sexuality, speciation and biogeography.
We have been engaged in systematic, phylogenetic and taxonomic work on diatoms since 1974, when David Mann began his PhD on the taxonomy of Nitzschia, Hantzschia and related genera. Since then the scope of our research has expanded, but we work mainly on raphid pennate diatoms, especially naviculoid genera and the Bacillariaceae. In the 1980s David Mann worked intensively on raphid genera for an overview of diatom biology and classification [F.E. Round, R.M. Crawford & D.G. Mann (1990) The diatoms. Biology and morphology of the genera. Cambridge University Press], for which he contributed most of the accounts of raphid genera and substantial parts of the Introduction. At the same time, he examined the potential of ontogenetic data in diatom systematics, and also the value of chloroplast and auxospore data, in which he was very ably assisted by Alan Stickle (1983-6). In the 1990s, Stephen Droop undertook detailed morphometric and ultrastructural studies of Diploneis, but much of this work remained incomplete when Stephen decided on a change of career. Stephen and Dr Helen Jones also worked towards a British Marine Diatom Flora (initiated by Professor Frank Round, University of Bristol), but this project was abandoned for lack of funds after work on Diploneis, Lyrella, Petroneis and Nitzschia and some others. We have used light and electron microscopy to examine cell wall morphology, as is usual in diatom taxonomy, but we seek also to incorporate studies of chloroplast morphology, nuclear structure and reproductive biology into our systematic research. We took part in two interdisciplinary projects (ADIAC and DIADIST) to investigate whether automated identification systems could be developed for diatoms, based on automated feature extraction from digital images and algorithms to compare the unknown specimen with databased images of species. Both of these projects achieved considerable success, to proof of concept, but did not progress to working systems. Now we increasingly make use of molecular genetic data in our systematic work, beginning in the late 1990s with rbcL studies by Dr Gillian Simpson. In 2010, Dr Shinya Sato came to Edinburgh to continue and expand his research on pennate diatoms and to expand his portfolio into cytology and barcoding.
In the 1970s, research on the sexual phase of the life cycle was rare. Most of the limited amount of work done since World War II had been done by just two researchers, Prof. Dr. Lothar Geitler in Vienna and Prof. Dr. Hans Adolf von Stosch in Marburg, together with a few colleagues (e.g. Prof. Dr. Elizabeth Tschermak-Woess, Dr Gerhard Drebes). There was a perception that sex was rare in diatoms and that a special magic was needed to find it. In the early 1980s, David Mann found that mud-dwelling epipelic diatoms often became sexual a few days after following transfer from nature to the laboratory. The factors responsible for the induction of sexual reproduction remain unclear, but the transfer to the laboratory certainly involved increased temperature and daylength. Sexualization took place in mixed populations harvested from the mud, which we therefore referred to as 'seminatural populations'; they often contained many species and within a species cells were often present representing different stages in the size-reduction cycle. Using seminatural populations, the sexual reproduction of several genera, e.g. Placoneis, Sellaphora, Lyrella and Petroneis, was observed for the first time, and extra detail discovered for many others, e.g. Neidium, Amphora. This information was used to inform the new classifications of raphid diatoms in Round et al. (1990) and has also been published in more detail in papers. In retrospect, it is fortunate that these studies were made on heterogeneous mixed populations because it led to the discovery of reproductive isolation between closely related diatoms within the same nominal 'species' (see below). It was also fortuitous because many raphid diatoms are heterothallic, so that it is often more efficient to study sexual stages in seminatural populations, rather than clonal cultures, because the natural populations are likely to contain both mating types.
The extent of heterothally has been a major surprise. We began a collaboration with Dr Victor Chepurnov, then at the Karadag Biological Station, Crimea (Ukraine), in the mid 1990s. Dr Chepurnov and his mentor, Dr A.M. Roshchin, worked independently from the western European tradition established by Prof. L Geitler and summarized in e.g. G. Drebes' summary of diatom sexuality [in a chapter in D. Werner (Ed.) (1977) The biology of diatoms. Blackwells Scientific, Oxford], which asserted that diatoms are homothallic, i.e. sexual reproduction can occur between cells of a single clone. Noting that some pennate diatoms do not reproduce sexually in monoclonal culture, Roshchin and Chepurnov experimented by mixing clones in pairs: they found that sexual reproduction occurred in some combinations of clones but not others. Further work by Victor Chepurnov and David Mann showed that this heterothally is common in pennate diatoms; indeed, it is quite likely to be the ancestral state for the whole group. Since the 1990s, other labs have also turned their attention to the sexual phase and Chepurnov and Mann have collaborated with several other groups, leading to joint publications with researchers in the Czech Republic (Prof. Dr Aloisie Poulíčková), Belgium (Dr Griet Casteleyn, Prof. Drs Koen Sabbe and Wim Vyverman), Japan (Prof. Masahiko Idei, Dr. Shigeki Mayama), Germany (Dr Shinya Sato and Prof. Linda Medlin), Italy (Drs Alberto Amato, Wiebe Kooistra and Marina Montresor) and the USA (Julie Koester, Prof. Susan Brawley, Dr Peter von Dassow). Subsequent studies in collaboration with Dr Rosa Trobajo (Spain) and Prof. Poulíčková have begun to reveal significant numbers of automictic diatoms. There is clearly much to be learned about sexuality in diatoms, which will in turn help us to understand how populations develop, evolve and spread. The potential of some model systems, e.g. Seminavis and Pseudo-nitzschia, for understanding the genetic regulation of life cycle progression and sexuality is rapidly becoming clear.
Although we and others have been successful in the last 30 years in observing sexual reproduction in cultures and seminatural populations of diatoms, it remains true that it is rare to find sexual reproduction in nature, even though every clone of most diatoms must eventually reproduce sexually (or via automixis). We have therefore sought to understand the dynamics of the diatom life cycle in nature and this can be done by using size as a marker. Because diatom cells get smaller during the vegetative phase of the life cycle and expand immediately and very rapidly after the sexual phase (or after automixis), size is a rough proxy for the time that has elapsed since the last sexual event. Consequently, analysis of the frequencies of different sizes of cells (= 'size spectra') and how these frequencies change with time can give good information about progression through the life cycle; a review of size spectra and life-cycle length was made by David Mann in 1988. There is now a small but dedicated, world-wide group of researchers interested in life cycle dynamics, loosely coordinated by Dr David Jewson, and we remain in contact with them.
Our research on speciation has focused predominantly on the genus Sellaphora, a group of mud-dwelling diatoms that is found throughout the world’s lakes, ponds and rivers. For more than two decades we have studied this genus, originally concentrating on local lakes, e.g. Blackford Pond, an ordinary duck pond in Edinburgh, and Threipmuir Reservoir, a dystrophic lake to the SW of Edinburgh in the Pentland Hills. More recently, we have broadened our sampling considerably, looking at ponds and lakes elsewhere in Scotland, and also in England, Belgium, the Czech Republic and Australia. Over the years, we have gathered a wide variety of data that demonstrate the existence of hidden (cryptic, semicryptic and pseudocryptic) diversity in Sellaphora and we have shown that some traditionally defined species are in fact composed of many 10s of species. In Blackford Pond alone, nine different species previously classified together in "Sellaphora pupula" live alongside each other without interbreeding, raising questions about how such similar forms are able to coexist without competitive exclusion. Studies of reproductive isolation were undertaken in the 1980s in seminatural populations, and then in laboratory cultures, during and after research visits by Victor Chepurnov. Molecular genetic studies, first by Carolyn Guihal and Gillian Simpson in Edinburgh, later by Dr Anke Behnke (working with Prof. Dr. Thomas Friedl in Göttingen) and especially Dr Katharine Evans working in Edinburgh (also Dr Alex Wortley), have subsequently greatly enhanced our understanding of species diversity in Sellaphora. We have collaborated with others (Victor Chepurnov, Aloisie Poulíčková, Rosa Trobajo, Alberto Amato and Marina Montresor, Griet Casteleyn, Pieter Vanormelingen) to examine other genera, including Neidium, Navicula, Amphora, Nitzschia, Pseudo-nitzschia and Eunotia, to see whether conclusions drawn from Sellaphora have any generality and to learn from these other systems and other research teams.
Because of the difficulties of identifying species microscopically (impossible with cryptic species!), we have been investigating the potential of DNA barcoding. Dr Katharine Evans led this project from 2005 to 2009 and found that the 'animal barcode', a region within the mitochondrial cox1 gene, performed extremely well in our test system, the genus Sellaphora. We also examined how barcodes might be formally linked to taxon names and made nomenclaturally effective as 'molecular types'. Two Synthesys-funded study-visits to Edinburgh focused on DNA barcoding, Pieter Vanormelingen successfully extended Sellaphora studies with a detailed examination of the correspondence of cox1 clades and reproductive isolation in the S. auldreekie species complex. Dr Rosa Trobajo examined the possibility of using the cox1 barcode in the taxonomically difficult genus Nitzschia, using the N. palea species complex, which she had already studied in detail using morphometrics, mating data and LSU rDNA analyses. Despite trials with different primers, it proved impossible to obtain cox1 sequences in several clones of the N. palea complex but rbcL was suggested as a possible alternative. Other researchers (Dr Monica Moniz & Dr Irena Kaczmarska, Mount Allison University; Sarah Hamsher, University of New Brunswick) have also been unsuccessful in attempts to use cox1 for barcoding and other markers are being sought.
From 2006 onwards, Dr Katharine Evans developed microsatellite markers to examine gene flow and population structure in Sellaphora, particularly in S. capitata and S. blackfordensis. Applying these, she was able to show that, although this species is very widespread, occurring in Australia and Europe (and probably elsewhere), populations are genetically differentiated from each other. Dispersal is not so rapid as to prevent divergence, and hence there may be many opportunities for speciation despite the fact that no populations can be considered to be allopatric in the conventional sense.
It remains unclear whether the narrow ranges of the many 'endemic' diatom species that have been described are (1) artifacts of poor sampling or poor taxonomy, (2) real, resulting from evolution in isolation because of poor dispersal, or (3) real, resulting from adaptation to a unique environment. For example, many supposedly endemic taxa have been described from Lake Baikal in Siberia and this may be because it is very old and isolated, so that many species have evolved in situ and have been unable to spread elsewhere, rather like the higher plants and animals of Madagascar. Against this, the area surrounding Baikal, and indeed huge areas elsewhere in Siberia, have not been studied in comparable detail so that the true geographical ranges of the Baikal 'endemics' are unknown. Also, the lake has a very unusual limnology, matched nowhere else in the world. Making progress in this field is particularly dependent on good taxonomy, and will also require autecological, phylogenetic and population genetics studies.
Royal Botanic Garden Edinburgh