Tales of Hofmann …

freshwater_benthic_diatoms_

For the past five years or so the constant companion on my desk whilst I stare down my microscope has been a thick tome (2.8 kg) entitled Diatomeen im Süßwasser-Benthos von Mitteleuropa by Gabi Hofmann and colleagues.  It serves as my aide-mémoire when I am analysing freshwater diatoms, jogging my memory when I see a diatom that I recognise but whose name I have forgotten.  Before this was published, I used a French publication Guide Méthodologique pour la mise en oeuvre de l’Indice Biologique Diatomées which was free to download (I cannot find a link on the web any longer, unfortunately).   Neither of these is the last word in diatom taxonomy, but that was not the point: a lot of the time, I just need a gentle reminder of the right name for the species I am looking at, and I don’t want to have to pore through a pile of books in order to find this.

One of the strong points of both books is that they are copiously illustrated, and the plates are arranged very logically so that similar-shaped diatoms are together, making it easy to pick out differences.   For most routine identification, this is exactly what is needed: we may pretend that we are logical people but, in truth, pattern matching beats using a key nine times out of ten.   The 133 plates in Diatomeen im Süßwasser … act as a visual index and, to make life even easier, the species descriptions are arranged alphabetically and cross-referenced in the plates.  Having found an image that resembles the diatom I am trying to identify, it is straightforward to flick to the description to check the details.

There is just one problem: Diatomeen im Süßwasser-Benthos von Mitteleuropa is in German, and quite technical German at that.   I tell people not to worry because all the images are in English but, in truth, I worry that I may lose some of the nuances due to my linguistic limitations.   I was delighted, then, to be asked by Marco Cantonati to help produce an English version of the book.  Marco is half-German so reads and speaks the language fluently, and I was able to work on his first drafts in English to produce the final text.   Conscious that translating a German book into English is only a partial solution for the almost 70% of the EU who have neither as their first language, we also unpicked the prose in order to put the information about each species into a series of “bullet points” so that it was more accessible and we also took the opportunity to update some of the taxonomy.   A large part of last weekend was spent poring over the proofs so it should not be long now before it is available to purchase.

The great irony for me is that I am putting the finishing touches to this book at the same time as I am helping the Environment Agency to move away from using the light microscope to identify diatoms altogether.   I am just finalising the last of the regular competency tests that I organise in which, Environment Agency staff will participate, after which routine samples will be sent off for Next Generation Sequencing rather than being analysed by light microscope.  I’ve written about the pros and cons of this before (see “Primed for the unexpected …”) but there is a funny side.   After over a decade of struggling with identification literature in a language that almost none of them spoke my dedicated band of Environment Agency analysts get the book they dreamed about two months after their last diatom slide is packed away.   My sense of timing is, as ever, impeccable …

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).   Diatomeen im Süßwasser-Benthos von Mitteleuropa. A.R.G. Gantner Verlag K.G., Rugell.

Prygiel, J.  & Coste, M. (2000).   Guide Méthodologique pour la mise en oeuvre de l’Indice Biologique Diatomées.   NF T 90-354.  Cemagref, Bordeaux.

A simple twist of fate …

surirella_spiralis_117024

Amidst the dreary nothingness of the sample that prompted the previous post, I stumbled across the diatom in the photograph above.  This image gives a misleading impression as it is a relative large diatom with considerable variation in three dimensions and my first thought was that I was looking at a fragment of vaguely diatom-like structures amidst a unfocussed blur.   Careful use of the fine focus control revealed the twisted nature of the structure and I was able to create this semi-focussed image from a “stack” of images of the individual focal planes using Helicon Focus software.   The scale bar is 10 micrometres (= 1/100th of a millimetre).  As there are relatively few diatoms with a frustule with such a contorted form, it was relatively easy to identify it as Surirella spiralis Kützing 1844.

Surirella spiralis is one of a small number of diatoms whose outline is twisted.   There are diatoms that show considerable curvature within a single plane (see Stenopterobia sigmatella in “Reflections from Ennerdale’s Far Side”) but few where this curvature occurs between planes.   The only other diatom with this feature that I have written about in this blog are Entomoneis (see “A typical Geordie alga …”) and Cylindrotheca (see “Back to Druridge Bay”).   These twisted diatoms, like sigmoid diatoms such as Stenopterobia, typically have motile habits.  In my post on Stenopterobia I wondered what advantage a sigmoid outline conferred on a diatom and we really need to ask the same questions when thinking about twisted diatoms.  I have the germ of an idea, but want to think it over some more before unleashing it onto the world.

Surirella, Stenopterobia and Entomoneis are all members of an order of diatoms, the Surirellales, that are the subject of a recent paper by Elizabeth Ruck, from the University of Arkansas, and colleagues.  They compared morphology and genetic differences amongst members of this order, along with a related order, the Rhopalodiales, two of whose members are Epithemia and Rhopalodia, both of which I have also written about in this blog.   Their conclusion is that current generic limits need an extensive shake up with long-established genera that seemed to be based on sensible criteria when viewed with the light microscope split apart and reassembled, based on ultrastructural and genetic characteristcs.

The main changes relevant to a freshwater ecologist are as follows:

  • Campylodiscus: some freshwater species retained in Campylodiscus, some moved to Iconella; marine species moved to Coronia. The Fastuosae group of Surirella are now included in Campylodiscus;
  • Cymatopleura: now included in Surirella
  • Entomoneis: no change
  • Epithemia: all species now merged into Rhopalodia;
  • Rhopalodia: now includes Epithemia;
  • Stenopterobia: now included in Iconella;
  • Surirella: now limited to the Pinnatae group of Surirella, plus former Cymatopleura species;
  • The genus Iconella has been re-established for a group of former Surirella species (section Robusta) along with some freshwater Campylodiscus species and Stenopterobia. Of particular relevance to this post, Surirella spiralis is now Iconella spiralis (Kützing) Ruck & Nakov in Ruck et al. 2016; and,
  • The order Rhopalodiales has been subsumed into Suriellales.

It will be interesting to see whether or not, and how quickly, these names diffuse through the community of scientists who study diatoms.   Taxonomy has a dual nature: on the one hand, specialists are driven by a desire to understand how evolutionary forces have shaped and differentiated a group of organisms; on the other hand, taxonomists act as biology’s janitors, sorting and organising information about species so that other biologists can use this for their own purposes.   I am the editor and co-translator of a guide to European diatoms that was being finalised just as this paper was published and which, as a result, uses the “old” names.   These books often have a ten or twenty year shelf life which will prolong the use of these names, and slow the uptake of new ones.   I also know, from many years training people to analyse diatoms, that taxonomic changes, however well justified, sow confusion among beginners.   On the other hand, we are entering a new era, when molecular barcoding will be used more widely for routine identification of diatoms and, for this, a correct understanding of the phylogenetic relationships amongst a group of organisms improves the accuracy of the bioinformatics routines that assign names to the diatoms.

For most practical purposes, in other words, Surirella spiralis will remain S. spiralis for some time (and Stenopterobia sigmataella will remain S. sigmatella too), if only because of the innate conservatism of most of the people who work with diatoms.   My use of the old name in this post means that the part of my readership who know at least a little about diatoms could place the diatom within a familiar framework, even if Iconella spiralis is the correct name.   The term “post-truth” has entered our political vocabulary over recent months; in diatom taxonomy and identification, however, we sometimes have to accommodate “pre-truth” as well.

References

Ruck, E.C., Nakov, T.., Alverson, A. & Theriot, E.C. (2016).  Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales.  Molecular Phylogenetics and Evolution 103: 155-171.

Ruck, E.C., Nakov, T.., Alverson, A. & Theriot, E.C. (2016).  Nomenclatural transfers associated with the phylogenetic reclassification of the Surirellales and Rhopalodiales.  Notulae algarum 10: 1-4.

 

Identification by association?

A few months ago, I wrote briefly about the problems of naming and identifying very small diatoms (see “Picture this?”).   It is a problem that has stayed with me over the last few months, particularly as I oversee a regular calibration test for UK diatom analysts.   The most recent sample that we used for this exercise contained a population of the diatom formerly known as “Eolimna minima”, the subject of that post.   Using the paper by Carlos Wetzel and colleagues, we provisionally re-named this “Sellaphora atomoides”.   Looking back into my records, I noticed that we had also recorded “Eolimna minima” from an earlier slide used in the ring test.   These had a slightly less elliptical outline, and might well be “Sellaphora nigri” using the criteria that Wetzel and colleagues set out.   There are slight but significant differences in valve width, and S. nigri also has denser striation (though this is hard to determine with the light microscope).   These populations came from two streams with very different characteristics, so there is perhaps no surprise that there are two different species?

Eolimna_minima_GMEP37111

A population of “Eolimna minma” / Sellaphora cf. atomoides from unnamed Welsh stream used in UK/Ireland ring test (slide #39)  (photographs: Lydia King).

The differences in ecology are what concern me here.   Wetzel and colleagues focus on taxonomy in their paper but make a few comments on ecology too.  They write: “The general acceptance is that S. atomoides … is usually found in aerial habitats (or more “pristine” conditions) while the presence of Sellaphora nigri … is more related to human-impacted conditions of eutrophication, pesticides, heavy metal pollution and organically polluted environments”.  This statement is worrying because it suggests that the ecological divide between these two species is clear-cut.   Having spent 30 pages carefully dissecting a confusing muddle of species, it strikes me as counterproductive to repeat categorical statements made by earlier scientists who they had just demonstrated to have a limited grasp of the situation.

The risk is that a combination of slight differences in morphology coupled with (apparently) clear differences in ecology leads to the correct name being assigned based on the analyst’s interpretation of the habitat, rather than the characteristics of the organism.   This is not speculation on my part, as I have seen it happen during workshops.   On two occasions, the analysts involved were highly experienced.  Nonetheless, the justification for using a particular name, in each case, was that the other diatoms present suggested a certain set of conditions, which coincided with the stated preferences for one species, rather than with those for a morphologically-similar species.

I have no problem with environmental preferences being supporting information in the designation of a species – these can suggest physiological and other properties with a genetic basis that separate a species from closely-related forms.  However, I have great concerns about these preferences being part of the identification process for an analysis that is concerned, ultimately, with determining the condition of the environment.  It is circular reasoning but, nonetheless, I fear, widespread, especially for small taxa where we may need to discern characteristics that are close to limits of the resolution of the light microscope.

Gomphonema exilissimum is a case in point.  It is widely-regarded as a good indicator of low nutrients (implying good conditions) yet there have been papers recently that have pointed out that our traditional understanding based on the morphology of this this species and close relatives is not as straightforward as we once thought.   Yet, the key in a widely-used guide to freshwater diatoms (written with ecological assessment in mind) contains the phrase “In oligotrophen, elektrolytarmen, meist schwach sauren Habitaten” (“in oligotrophic, electrolyte-poor, mostly weakly-acid habitats”) amongst the characters that distinguish it from close relatives.  The temptation to base an identification wholly or partly on an inference from the other diatoms present is great.

Including an important environmental preference in a key designed for use by people concerned with ecological assessment brings the credibility of the discipline into question.   Either a species can be clearly differentiated on the basis of morphology alone, or it has no place in evaluations that underpin enforcement of legislation.   That, however, takes us into dangerous territory: there is evidence that the limits of species determined by traditional microscopy do not always accord with other sources of evidence, in particular DNA sequence data.   These uncertainties, in turn, contribute to the vague descriptions and poor illustrations which litter identification guides, leaving the analyst (working under time pressure) to look for alternative sources of corroboration.  I suspect that many of us are guilty of “identification by association” at times.   We just don’t like to admit it.

References

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).  Diatomeen im Süßwasser-Benthos von Mitteleuropa.  A.R.G. Gantner Verlag K.G., Rugell.  [the source of the key mentioned above]

Wetzel, C., Ector, L., Van de Vijver, B., Compère, P. & Mann, D.G. (2015). Morphology, typification and critical analysis of some ecologically important small naviculoid species (Bacillariophyta).  Fottea, Olomouc 15: 203-234.

Two papers that highlight challenges facing the identification of the Gomphonema parvulum complex (to which G. exilissimum belongs) are:

Kermarrec, L., Bouchez, A., Rimet, F. & Humbert, J.-F. (2013).  First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta).   Protist 164: 686-705.

Rose, D.T. & Cox, E.J. (2014).  What constitutes Gomphonema parvulum? Long-term culture studies show that some varieties of G. parvulum belong with other Gomphonema species.  Plant Ecology and Evolution 147: 366-373.

Picture this?

Teesdale_desmids_linocut

A curious moment of serendipity saw me stuffing a new scientific paper into my bag to read on the train as I travelled to a workshop on reduction linocut printing. A second instance of serendipity occurred when I walked close to the site of Thomas Bewick’s studio in Newcastle as I contemplated the contents of this paper whilst walking from Newcastle Station to Northern Print‘s workshop in the Ouseburn Valley. I was, clearly, destined to write a post on natural history illustration, and the problems of reproducing images.

The paper I was reading related the efforts of Carlos Wetzel and colleagues to understand the taxonomy and nomenclature of a group of very small diatoms, historically placed in the genus Navicula but more recently spread between Sellaphora and Eolimna. The problem they address is essentially one of calibration: do the names we use for modern diatoms correspond to the organism to which the name was first applied, or has our understanding of that species gradually ‘drifted’ over time so that we now use it either for a different species altogether, or for a number of species that match the original description?

The plate below puts the problem into perspective. It shows a number of specimens corresponding to the description of what we thought was Eolimna minima at the time, though should now probably be called Sellaphora nigri. These cells are mostly less than a hundredth of a millimetre in length, have a linear-elliptical outline and few surface features that can be resolved easily with the light microscope.    Small variations in the valve outline and the density of striae had encouraged diatomists to establish new species and varieties until there were a large number of names in circulation and it was not always easy to separate the wheat from the chaff.   Wetzel and his colleagues had tracked down the original descriptions and the “type material” (the specimens that formed the basis of these original descriptions) in an effort to sort out the mess.

Eolimna_minima_StMawgams

Sellaphora nigri / Eolimna minima from Menahyl River, St Mawgan Bridge, Cornwall, September 2009. The scale bar is approximately 10 micrometres (= 1/100th of a millimetre) long.   Specimens are arranged into two “morphotypes”: “narrow” and “blunt”.   Photographs: David Mann.

Our understanding of diatoms is driven in large part by the technology available to scientists at any point in history. Not surprisingly, the first diatoms to be described tended to be the larger species, relatively speaking, and it is no surprise that the earliest descriptions of the very small forms that are the subject of this post are rather basic.   These date back to Kützing in 1849, Rabenhorst in the 1850s and Grunow in the 1860s, all of whom would have had relatively basic microscopes by modern standards, and who worked without electric light with which to illuminate their specimens. They also did not have access to high resolution mountants, which only became available in the middle of the twentieth century. Nor were they able to photograph their specimens and, indeed, any drawings that they made would have had to be passed to a specialist engraver, who would have transferred the image either to a woodblock (using the ends of hard woods such as box and cherry rather than cutting into the grain) or a metal plate.   So there would have been at least two steps between the observer’s initial view of the diatom and the published illustration which, in the case of diatoms such as these, was working right at the edge of the resolution of the light microscopes of the day. It is no surprise, then, that the organism that Kützing described as “Synedra minutissima” and which later workers considered to be a small Navicula has subsequently bounced through several genera (and families), before Wetzel and colleagues decided on the basis of light and electron microscopical observations of Kützing’s original material that it probably belonged to Halamphora.

Image reproduction is, I suspect, almost as significant as optical technology in determining the rate of advances in understanding of diatoms. You only have to look back at papers in Diatom Research published only 20 years ago, and compare both the quality and quantity of images to understand this. Photo-editing packages such as Photoshop and CoralDraw are the unsung heroes of modern diatom taxonomy, enabling images to be edited and rearranged in multiple combinations.   We can now do in a couple of hours what would have taken weeks of time for an engraver in the 19th century, capturing images of a quality that would have been beyond Kützing’s wildest dreams.   Having done this, we can then discuss the results via email and Skype with people in other countries, or even different continents.

Yet there is one final twist to this tale: the plate of Sellaphora nigri / Eolimna minima is one of a series of plates that David Mann put together last year whilst he and I were pondering some RbcL sequences from field populations.   The genetic information seemed to be telling us that there were several distinct genotypes within complexes that we were identifying, with the light microscope, as Eolimna minima.   The scale of difference was such as to suggest that these genotypes may well be distinct species, albeit barely discernible even with the very best light microscopes available. We put that work aside, distracted by other, more pressing tasks, but I dug out the plates when thinking around the issues I’ve discussed in this post.   So it is quite possible that we have still not solved all the mysteries of this group of tiny, but very common, diatoms.

Reference

Wetzel, C.E., Ector, L., van de Vijver, B., Compère, P. & Mann, D.G. (2015). Morphology, typification and critical analysis of some ecologically important small naviculoid species (Bacillariophyta).   Fottea, Olomouc 15: 203-234.

More about the life and work of Thomas Bewick in:

Uglow, J. (2006). Nature’s Engraver: A Life of Thomas Bewick.   Faber and Faber, London.

The picture at the top of the post is the result of my labours at Northern Print. It is a reduction linocut (also known as a “kamikaze linocut”, as the plate is destroyed during the production of the image) showing desmids from Upper Teesdale (see “Abstraction and Reality in Upper Teesdale”)

When is a diatom like a London bus?

This post takes us back to Semer Water (see “Lake Lakelake Lake”) for a closer look at some of the diatoms that live in the littoral zone.   I studied this lake back in 2012 as part of a project funded by Natural England, and recently used one of the samples collected as part of that study for a “ring-test” amongst diatomists involved in routine ecological assessment in the UK and Ireland. This provides an opportunity for a number of experienced analysts to take a detailed look at the diatoms present in a sample and compare notes.

Between us, we found over 90 different species that we could name in a single sample, amongst which there were a number that caused us no disagreement and a few where we struggled to achieve a consensus.   And there was one group where we achieved a consensus of sorts insofar as the entities that we found matched the pictures in the latest reference works, but shared a sense of misgiving about whether the names we used told the whole story.   The diatoms that caused these problems were representatives of a group of small diatoms that, for a long time, were grouped in the genus Fragilaria but which, following a paper by David Williams and Frank Round in 1987, were split between several different genera including Pseudostaurosira, Staurosira and Staurosirella.   This generated some controversy although, as the dust settled, most people agreed that these taxa definitely did not belong in Fragilaria, even if the exact allocation of species between the genera continued to excite debate. The plate below shows three “species” that we found in Semer Water although the suspicion is that the seven forms I’ve called “Staurosirella pinnata” may represent several different species.

Semer_Pseudostaurosira_Stau

Small Fragilaroid diatoms from the littoral zone of Semer Water August 2012.   A. Pseudostaurosira brevistriata; b. Staurosirella leptostauron; c. – i. different morphotypes within the “Staurosirella pinnata” complex. Scale bar: 10 micrometres (= 1/100th of a millimetre).

However, my purpose today is not to get bogged down in the minutiae of these nomenclatural squabbles but to take a step back and look at their ecology.   Members of this complex are widely distributed across a wide range of water type but they are particularly abundant in hard waters, both standing and running.   What interests me is that they often seem to occur together.   Hence the title of the post: like London buses, you wait ages for one small Fragilaroid species to appear in a sample, and then three come along at once…

In order to test this association, I searched my database and found 705 records where at least one of the more common species in the complex were found (out of a total of 3838 records).   309 (44%) of these contained more than one species, but this figure leapt to 82% when I only considered samples where the sum of these species exceeded two per cent, and a mighty 98% when I just included the 90 samples where the sum exceeded ten per cent.   You can see this trend clearly in the graph below where I have plotted the percentage of one species against the sum of the percentages of the other four that I have considered.   The issue gets more complicated when we consider that some of the so-called species could, themselves, be complexes of several species that can co-exist (as in the case of Staurosirella pinnata in the plate above).

Semer_London_buses

Co-variation in relative abundance of common Fragilarioid species. Each plot shows the percentage of one species (or species complex) on the x axis, and the combined percentage of the other four species on the y axis. Log scales are used for the sake of clarity.   a. Pseudostaurosira brevistriata; b. Staurosira construens (and varieties); c. Staurosirella leptostauron; d. Staurosira elliptica ( = Pseudostaurosira trainorii); e. Staurosirella pinnata complex.

What is going on here?   If they all live in the same habitat then, in theory, the “competitive exclusion” principle should work to eliminate all but the fittest.   That two or more appear to co-exist on a regular basis suggests that they are occupying distinct niches that we are not recognising with our usual methods of studying the microscopic world of lakes and rivers (see “Baffled by the benthos (1)” and “Baffled by the benthos (2)”).   It might be a physical niche, but the niche could also be defined by chemical or biological factors.   Could it be, for example, that these different but (fairly) closely-related forms differ in their levels of resistance or tolerance to fungal or viral infections?   Or do they have subtle variations in the amount of light that each needs, but which are obliterated by our unsubtle sampling methods?

The result is the diatom equivalent of a “perfect storm”: neither the taxonomy nor the ecology are described with any great clarity.   It is possible that a better understanding of the taxonomy will lead to a more nuanced appreciation of their ecology. Taxonomists often dangle this bait, but the sad truth is that there are few cases where ecologists emerge blinking into the light after the taxonomists have finished their fiddling. But ecologists must take their share of the blame, being very conservative in the methods that they use to deduce ecological differences between species.   I could, in fact, use my 1930 edition of the Süsswasserflora vön Mitteleuropa to identify this group of species and, apart from the name changes, reach exactly the same  conclusions as I might have done 85 years ago.

Thanks to Ingrid Jüttner (National Museum of Wales) for the diatom photographs, and Eduardo Morales (Bolivian Catholic University, Cochabamba, Bolivia) for taxonomic assistance.

References

Williams, D.M. & Round, F.E. (1987).   Revision of the genus Fragilaria. Diatom Research 2: 267-288.

A flavour of the subsequent debate is given in:

Morales, E.A. & Trainor, F.R. (2008). A new paradigm for freshwater fragilarioid diatom classification? A critique of Lange-Bertalot’s new system. Journal of Phycology 37 (supplement): 36-37.

And another one …

I encountered yet another instance of a species that had dropped out of the collective consciousness of biologists last week, with some help from colleagues Lydia King and Luc Ector.   I co-ordinate an exercise whereby all those of us who analyse diatoms regularly for ecological assessments in the UK and Ireland calibrate themselves against one another. The last sample that we used for this exercise came from a small stream in County Tyrone, Northern Ireland, and it contained a mess of Fragilaria species that proved to be rather challenging. Some we could name quite easily, others took a little more work.   Amongst these Fragilaria species was a nice population of Fragilaria vaucheriae, with its distinct one-sided central area, linear-lanceolate outlines and coarse striae. This was close in all respects to the type description, and presented us with few challenges.

115011_Fragilaria_vaucheria

Fragilaria vaucheriae from Trillick Tributary, Carran Bridge, County Tyrone, Northern Ireland, May 2014. Scale bar: 10 micrometres (1/100th of a millimetre). Photographs: Lydia King.

However, there was also a number of valves in the sample which were similar in many respects to the description of F. vaucheriae in the standard floras, but was slightly narrower and which had a more lanceolate outline.   Confusingly, a very similar diatom is illustrated in the 1991 edition of the bwasserflora von Mitteleuropa as one of a number of illustrations of “Fragilaria capucina var. vaucheriae”.   Our sample, however, had two distinct populations: the broader valves which correspond to “true” F. vaucheriae and the narrower ones that many of us, using the bwasserflora, have “lumped” into F. vaucheriae simply because there were no more plausible alternatives on offer.

Luc Ector eventually pointed us towards descriptions and illustrations of another species, Fragilaria pectinalis, which does look very similar to Lydia’s photographs.   Our only slight concern is that the stria density in our population is slightly lower than in the description of the type population of F. pectinalis.   For this reason, we are referring to our population as “Fragilaria cf. pectinalis”, until we are more certain.

115011_Fragilaria_pectinali

Fragilaria cf. pectinalis from Trillick Tributary, Carran Bridge, County Tyrone, Northern Ireland, May 2014. Scale bar: 10 micrometres (1/100th of a millimetre). Photographs: Lydia King.

Fragilaria pectinalis is an interesting case study in the rise and fall of species names.   This species is the type species for the genus Fragilaria, meaning that it was the first species in the genus to be formally described (by Lyngbye in 1819).   It was known from even earlier, albeit under a different name, Conferva pectinalis, although the earliest illustrations are very schematic and hard to interpret.   What is interesting is how it disappeared from Floras and identification guides throughout the 20th century. It is not in Hustedt’s first edition of the bwasserflora von Mitteleuropa, nor is it in West and Fritsch’s Treatise on British Freshwater Algae (1927), Patrick and Reimer’s Diatoms of the United States (1966) or the second edition of the bwasserflora, as I have already mentioned. I suspect that it has generally been lumped into Fragilaria vaucheriae for most of this time. It is only thanks to the detective work of Akihiro Tuji and David Williams that has managed to bring the name back into circulation.

The next step, I guess, is to get it into the standard identification literature again.   My experience is that busy ecologists often do not have the time to trawl through the vast and rather dispersed primary literature every time they encounter a form that they do not recognise.   Hence they exhibit a tendency to squeeze forms into the closest category in the books that they do have.   Luc Ector has started the wheels rolling by including it into his recent publication but perhaps we’ll also see it in the next edition of Diatomeen im Süßwasser-Benthos?  

References

Bey, M.-Y. & Ector, L. (2013). Atlas des diatomées des cours d’eau de la région Rhône-Alpes. Direction régionale de l’Environnement, de l’Aménagement et du Logement Rhône-Alpes. http://www.rhone-alpes.developpement-durable.gouv.fr.

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011). Diatomeen im Süßwasser-Benthos von Mitteleuropa. A.R.G. Gantner Verlag K.G., Rugell.

Tuji, A. & Williams, D.M. (2006b). Typification of Conferva pectinalis O. F. Müll. (Bacillariophyceae) and the identity of the type of an alleged synonym, Fragilaria capucina Desm.   Taxon 55: 193-199.

Tuji, A. & Williams, D.M. (2008). Examination of types in the Fragilaria pectinalis – capitellata species complex.   Pp. 125-139. In: Proceedings of the Nineteenth International Diatom Symposium 2006 (edited by Y. Likhoshway).   Biopress, Bristol.

 

What’s in a name?

I’ve been thinking a lot recently about how the data ecologists collect moves through organisations and influences the decision-making process (see the chain of three posts starting with “The human ecosystem of environmental management“). And I’ve returned to that subject whilst preparing for a workshop in Cardiff where we are starting to put together an online Flora of the freshwater diatoms of Britain and Ireland. The project is being co-ordinated by Ingrid Jüttner of the National Museum of Wales, with financial support from the British Phycological Society.   It is a big task, because so many new species of diatom have been described over the past twenty years or so, and many existing species have been shuffled into different genera. The current situation is, frankly, bewildering for the frontline ecologists who have to analyse samples from around the country as part of ongoing assessments of river health.

The problem I’ve been addressing in my posts could be summarised as the ecology of information. An ecologist stands in a stream or (more likely) sits in a laboratory processing samples. S/he finds a preponderance of organisms that are indicative of a polluted river. How does that observation then move through the organisation and influence a decision on the management of that river?   My earlier posts considered this in very general terms; now I want to look in more detail at the issues concerning recording biological data, because the first step a frontline biologist takes after completing a survey or analysing a sample is to add the results to a computer database. But this is where the complications start.

Most of the identification literature written before about 1990 included a common species called Synedra ulna.   Since this time, however, there has been a dispute about the correct name of this species (summarised in the paper referenced below).   The widespread view now is that the correct name (albeit based on a rather pedantic interpretation of the International Code of Botanical Nomenclature) is Ulnaria ulna.   The species is the same; only the name has changed. This debate was continuing as we put together the current UK assessment tool, DARLEQ, and we adopted a conservative position, sticking with the name Synedra ulna.

This means that the software associated with this tool, and the underlying databases operated by the environmental agencies, all included the name ‘Synedra ulna’ but not the name ‘Ulnaria ulna’. Fast forward a few years to our new diatom Flora where we follow current practice and use the name Ulnaria ulna. Analysts who use our Flora will then record this name, not Synedra ulna, in their notebooks but then run into a problem when they want to add this name to the database, because it is not in the list of names that they are offered.

This is one of the points where the practice of an academic researcher and a biologist in a large organisation such as the Environment Agency diverges. Like many researchers, I have a database where I store my records but this is a low-key affair that is stored on my desktop. It is easy for me to open the file where I store the name of species and add one or two more each time there is a change in our understanding. When a single database serves a large organisation with legal responsibilities, the system has to be very secure and protected against well-meaning individuals tinkering with the mechanisms. That makes it harder to keep up-to-date with taxonomic and nomenclatural changes; more so when budgets have been slashed across the public services.

The problem is further compounded because biologists have to download data from the main database (“BIOSYS”, in the case of the Environment Agency) in order to load it into the standalone package, “DARLEQ”, that calculates the diatom indices. Whatever changes are made to BIOSYS, therefore, need to be mirrored in DARLEQ, else the software will not pick up all the data when it calculates indices.   Finally, whatever happens in England also needs to be done in Scotland, Wales and Northern Ireland, as the environment is a responsibility of the devolved administrations whilst the UK as a whole still presents a unified front to Brussels.

In theory, there is a single “hub”, the National Biodiversity Network, which links all names to a code which can then be used in databases across all organisations to link biological data with site and sample information. However, the NBN still needs to be fed information on changes to particular groups of organisms by specialists and this is where the system has broken down.   It is a problem that I have touched on before: there is no single authority for the diatoms who can arbitrate on additions or changes to the diatom flora of Britain and Ireland.   The tradition of biological recording, often underpinned by enthusiastic amateurs around the country, simply does not exist for this group (though it is worth remembering that the current, somewhat dated, checklist was the product of Bernard Hartley, an amateur).

I’m hoping that one of the functions of the Flora project team will be to act as the de facto “authority” that can feed changes to the NBN and, through them, to the environmental agencies and others who use diatoms. I would go further: the online Flora will not, actually, fulfil its ambition of reducing errors during ecological assessments unless there is a pathway through which these changes can be disseminated to the database managers who are the custodians for all the ecological information that has been collected over the past 25 years or so.

This, then, is the ecology of information in practice. Just as a pure ecologist wants to understand the structure of an ecosystem, and how all the parts relate to one another, so applied ecologists also need to be aware of how data and information (the “energy” in our bureaucratic ecosystems) gets from the field notebooks of scientists to the managers tasked with making decisions about environmental regulation. To push my analogy just a little further, small changes in biological nomenclature have the potential to make data unpalatable to the computer programs that “graze” on the results of our hard work. It should not be a big deal, if handled wisely, but budget cuts mean that this cannot always be taken for granted.

Reference

Hartley, B. (1986). A check-list of the freshwater, brackish and marine diatoms of the British Isles and adjoining coastal waters. Journal of the Marine Biological Association of the United Kingdom 66: 531-610.

Williams, D.M. (2011). Synedra, Ulnaria: definitions and descriptions – a partial resolution. Diatom Research 26: 149-153.