Wednesday, 20 February 2013

Wednesday wildflower: stinky little cress

When I was a kid, a favourite activity was to plant out a mix of mustard (Brassica nigra) and cress (Lepidium sativum) seed on a wet flannel in a saucer.  In a few days, a lawn of seedlings could be harvested for delicious tangy sandwiches.  The first thing that happens is the seeds swell and the cress seeds develop a blob of jelly—mucilage— around them.  Many of the family (Brassicaceae) have specialised mucilage bodies in their epidermal cells, and the mucilage they produce both glues them to the substrate and surrounds them in a moisture-holding layer.
Wart cress, Lepidium didymum.
Cress is the best known of many species in the genus Lepidium.  We have a good range of both native species (more on them another day) and weedy introduced ones.  Until recently the genus has been characterised by having small squat seed pods that open to release one seed from each half.  The reduction to one seed in each half of the pod makes them quite different from most of the rest of the family, which have long skinny pods with many seeds in each half.  But a few other genera, notably Cardaria and Coronopus (wart cress), have one seed per half; the only difference is they don't open.  And lately these have been shown to be simply non-opening Lepidiums.  That is, they've evolved from Lepidium ancestors by losing the line of weakness that allows the fruits to open.  So now these small genera are included in Lepidium.
Lepidium didymum flowers have just two functional stamens, but they're just like many other Lepidium flowers.
We have two wart cresses in New Zealand, Lepidium didymum and L. squamatum.  In both, the fruit splits into two one-seeded portions, but the seeds are not released from the fruit.  They also smell pretty unpleasant; you wouldn't want to put wart cress in a sandwich.
Lepidium didymum fruits don't open; instead they split into two one-seeded portions.
Loss of dehiscence (opening) is actually pretty common in the plant world, and because sometimes it leads to a fruit that looks and behaves very differently from those of close relatives, it can lead to misleading classifications if those striking differences are emphasised.  These Lepidiums are closely related to different-looking plants that have opening fruits.
Cardamine lacustris fruits are short and squat and they open slowly, unlike the slender explosive ones of other species of Cardamine.
The same thing happened in Cardamine, another genus of Brassicaceae that's characterised by explosively-opening fruits.  In the days before DNA sequencing, I made the wrong call about a newly-discovered native plant.  It looked like a Cardamine, but its fruits opened without the characteristic explosion, and so I assumed that meant it wasn't a Cardamine.  I named a new genus, Iti, for this plant.  More recently, DNA sequencing has shown its true relationships and it's been reclassified in Cardamine, as C. lacustris (Heenan 2002).


Heenan, P.B. 2002. Cardamine lacustris, a new combination for Iti lacustris (Brassicaceae).  New Zealand Journal of Botany 40: 563–569

Thursday, 14 February 2013

Elingamita johnsonii

The Three Kings Islands sit a bit north of North Cape, and they have a few peculiarities in their flora.  Two of them, Cordyline kaspar and Piper melchior, are named after two of the biblical three kings (the aliteration was lost when the genus Macropiper was combined with Piper recently).  Altogether, there are reckoned to be 13 endemic plant species on the Three Kings, very high for such a small area of land.

Two of them, Pennantia baylisiana and Tecomanthe speciosa, must be the world's equal rarest plants, because both are known from only single individuals on the Three Kings Islands.  You could argue that P. baylisiana is even rarer because the only plant is a female; however somehow it occasionally produces fruits which are a prospect for its reintroduction in the wild.  Both are well established in New Zealand gardens.
Elingamita johnsonii in my garden.
Elingamita johnsonii is another Three Kings endemic, but it's known from a few dozen plants.  It's classified in the Myrsinaceae, along with our native species of Myrsine, to which it's thought to be very closely related.

The plant in my garden is a male, and I've had it about 20 years.  For some of that time it lived in a pot in my office, where it suffered badly from scale insects.  After a while I took a risk and planted it out in the garden, and it hasn't looked back.  Now I'm having to build a dog-leg in a new retaining wall, to avoid burying its roots.

Elingamita johnsonii, male flowers starting to open
This year it's flowering heavily.  The flowers seemed to open a few weeks ago, with prominent large golden anthers, but these have sat for a long time without shedding pollen.  When I read the original description, I noted the flowers were said to have long stamen filaments, and now, after doing nothing for a few weeks, the filaments are elongating and the anthers opening to release their pollen.  The lower parts of the flower are also turning pink.  Although male, these flowers seem to have quite a well-developed ovary, style, and stigma, but I've never had fruit from this tree.
Elingamita johnsonii, male flowers.
Tītoki male flowers delay the final development and opening of their anthers in much the same way.
Elingamita johnsonii, a male flower soon after opening
Elingamita johnsonii.  At a later stage, when the filaments begin to elongate (right) and the anthers release their pollen (left).
The flowers are said to be quite different from those of Myrsine.  First the petals are joined into a short skirt-like tube; you can see it in the photo above.  Secondly, the stigma is small, with a little depression in it, punctiform.  In Myrsine, the petals don't form a skirt-like tube although they may be partly joined (see below) and the stigma is large and broader than the style.  These differences might not be very major in a genetic or developmental sense, and they probably reflect something about the pollination biology of these plants, rather than telling us much about their relationships.
Myrsine australis female flower.  Note the expanded stigma (out of focus in the centre).
Myrsine australis male flower.  Note that the four petals are shortly joined into a tube
If you're thinking about classification, here's a familiar dilemma.  E. johnsonii flowers look different from those of Myrsine, yet a Massey University PhD thesis by Karen Stöckler indicates Elingamita is very closely related to New Zealand species of Myrsine.  You'll know if you've read my previous postings on Veronica and Lobelia that I am strongly in favour of classifying plants with their nearest relatives rather than with look-alikes.  Interestingly, Pennantia baylisiana was similarly once classified in its own genus Plectomirtha.  Karen and I are collaborating on considering this question.

How did Elingamita come by its name?  It's named after the S.S. Elingamite, which ran aground in 1902 on West Island in the Three Kings, with the loss of forty-five lives.  One other native plant I know of commemorates a shipwreck: Lepidium naufragorum, a coastal cress.  The name refers to cast-aways, nine (correction 16 Feb 2013: the accounts I've linked to say ten) sealers who were dropped on the Open Bay Islands in 1810.  Their ship was never seen again, but they were rescued after 4 years of hardship.
Lepidium naufragorum.

Tuesday, 5 February 2013

The citation gap and its effects on taxonomy.

Ask any taxonomist, "Who's doing taxonomy nowadays?", and they'll tell you the same story: hardly anyone.  Funding for taxonomy is drying up in favour of research that'll turn a quick buck or research that explains rather than describes, or, crucially, research that brings in big overhead funding to institutions.

Look in many university biology departments to see who's teaching taxonomy, and the answer is: nobody.  If they have a systematist or two, most likely they'll be doing and teaching molecular phylogenetics.  I'm not knocking molecular phylogenetics; it's critically important work, but there are very few people now cataloguing and describing species, providing identification tools, curating collections, and databasing biodiversity, nor is anyone teaching those skills.

Ask a recent graduate what they learned about biological identification, classification, diversity, and even phylogeny, and likely you'll get a blank look.  Ask what the "C" in C. elegans or the "E" in E. coli stands for.  What's the species name for the Drosophila or Arabidopsis they're experimenting with?  Yet they'll use and misuse organisms' names throughout their careers to retrieve and organise knowledge and to describe their own research.

Sometimes, I don't think our biological colleagues do us any favours either.  In private they might sneer at what we do: it's stamp collecting; only nerds read our papers; it's nit-picking name-changing.  But it's what they do in public, or more accurately what they don't do, that really undermines this essential discipline of science.

What they don't do is cite taxonomists' work.  This is perhaps largely unintentional, but it has a profound effect.  There are a number of reasons.

1.  Taxonomists, like other scientists, publish their research in peer-reviewed journals.  New species have to be named—so other scientists can find and refer to information about them—and they have to be classified—so we can understand what they're related to.  Peer review is a check (not always an effective one, as in any discipline) that the work has been done well.  But the geneticist in the lab or the ecologist or conservationist in the field rarely reads these original papers.  You'd need a whole library to cover the plants or animals of any field site.  So they use the secondary literature: Floras, field guides and on-line resources like databases.  And these are what they cite, if they refer at all to the taxonomic foundations of their research.  Often, large chunks of those Floras, field guides, and databases have been simply copied from the primary literature; and their authors may happily take credit, along with the glory that comes with being cited a lot.  But the original authors, the ones that did the primary research, may rarely be cited, and that affects their careers.  (The plagiarism isn't the main issue that concerns me here, but it does concern me deeply; even when the original source is cited I still see substantial copying as plagiarism.)

I can illustrate this citation gap from my own publications.  Only one has been hugely cited: Flora of New Zealand Vol. 4 (Webb et al. 1988).  (And I must add, in relation to my comment above, that we took great pains—more pains than most readers will ever be aware of—to make sure the descriptions and keys in that book were all original and accurate for New Zealand material.)  It's been cited over 660 times in the scholarly literature (Google Scholar), and tellingly, another 17,000 times in the literature that's not covered by Google Scholar.  At the other extreme, a paper Bill Sykes and I wrote (Sykes & Garnock-Jones 1979) in which we reclassified the native Eugenia maire as a species of Syzygium has been cited just twice in the scholarly literature; you'd think it was a worthless piece of research if you believed the standard measures.  Yet our findings have been used by other biologists; the name Syzygium maire has been used in 119 scholarly papers and in 12,000 other publications and on line.  That reclassification places swamp maire more accurately among its relatives (including the clove); it's not trivial.

2.  There's a convention in biological publishing, which most journals blindly (and perhaps ignorantly) insist their authors follow (Garnock-Jones & Webb, 1996).  That is, when you use a biological name, you also must include the citation of the author who first used that name in that context (as if it were part of the name, which it isn't).  For example, in most scientific journals the name Ranunculus altus must be extended by adding the abbreviation of the describing author's name, in this case me: Ranunculus altus Garn.-Jones.  Why do it?  Well, it's a short-hand bibliographic citation that was used by the early taxonomists like Linnaeus, Banks, de Candolle and others to refer to each other's work in the days before scientific journals.  It doesn't have much meaning nowadays except for the rare circumstance where you need to distinguish between two plants that have the same name: Ranunculus altus Garn.-Jones is a different plant from Ranunculus altus (Julin) Ericsson.  But nowadays when we scientists are supposed to cite all our sources in the reference list at the end of the paper, the old-fashioned author citation convention lets researchers off the hook of citing their taxonomic sources.  And when the value of research work is (gu)estimated by the number of times it's cited in the scholarly literature, this puts taxonomists and taxonomy at a distinct disadvantage.

3.  Sometimes our work gets taken for granted or not cited for other reasons.  Maybe the names and classifications are just taken as a given that doesn't need to be referenced; maybe writers simply don't appreciate the research and expertise behind the names they're using.  Maybe they just don't think it's important enough.

Sometimes the journals themselves restrict the number of references that can be cited, and taxonomy can suffer through this too.  For example, a recent research paper in New Zealand used published phylogenetic taxonomy research as its raw data; the authors could not have done the study without it, but were any of those papers cited?  No, not one, unless you count citation in the supplementary data, which of course doesn't get noticed for the citation indices and impact factors that govern scientists' careers and universities' hiring decisions.  To be fair, those authors' hands were probably tied by the journal's reference limitation policy; it only allows a total of 12 cited references (a policy that might be deviation amplifying, to the advantage of high impact journals).  But the authors presumably made the decision to cite their ecological colleagues in the "proper" references that count, and to relegate their taxonomic colleagues to the supplementary list that doesn't (I am not citing that paper here because it's unfair to single out just one.)

4.  The worth of scientific journals is quantified using "impact factors". The impact factor of a journal in any year is the number of times it was cited divided by the number of papers it published.  Because taxonomists' work doesn't get cited as often as it should (explained above), the journals that publish taxonomic research tend to have low impact factors.  I've heard it said that some "top" journals are no longer publishing taxonomic papers, because taxonomy lowers their impact factors, but I haven't seen proper evidence for this.  Publishing in low impact factor journals is the kiss of death to a research career.  When academics review applications for positions, their judgement of applicants' worth is heavily slanted by the impact factors of the journals they publish in; and looking those statistics up is an easy alternative to the hard work of actually reading the applicants' papers.  The same thing happens when researchers apply for funding.  And there too, the funding body needs to demonstrate its relevance by funding researchers and topics that are likely to get published in high impact journals.  Researchers that can't pull big grants and don't publish in top journals are dead in the water; worse, they're shark bait.

How does this translate into employment trends and funding decisions?  The research success of academic departments and government research labs is increasingly judged by the quantity and quality of their researchers (in New Zealand the university research grading exercise is the PBRF and it's almost the only area of departmental funding that can go up or go down, now that income from student fees is capped) and by the external funding they can attract.  Journal impact factors are hugely important in the PBRF assessment.  PBRF scores directly affect the funding a department and a university will get, and in New Zealand, individual academics are graded, not the departments/disciplines as in the UK.  So departments are caught in a trap.  Even if they're wise enough to see the importance of taxonomy to their students' biological literacy, they simply can't afford to employ taxonomists any more; they're forced to go for a higher-profile discipline and maybe even drop their systematics courses.  Even though the lion's share of university funding is still given for teaching students, the discipline breadth and quality of teaching and the employment success and quality of graduates are rarely measured or questioned with anything like the effort that currently goes into the PBRF.

As systematics researchers are a dwindling pool, there are fewer people to cite their papers, unless ecologists and other biologists change their habits.

Why does this matter?  As the world's population grows and ecological relationships unravel under the stress, our understanding of the diversity of life on earth is becoming more and more critical.  Many countries face increasing extinctions of wildlife, which we wouldn't even be able to document, let alone avoid or repair, without taxonomy.  If that sounds like a bold claim, think about it for a while.  Without taxonomic descriptions, catalogues, and classifications of all those plants, animals, fungi, protists, and microbes, who could possibly notice that some are going extinct; we wouldn't even have recognised extinction as a general phenomenon.

And then, where are the new foods and drugs going to come from?  Who will identify the pests and diseases that threaten agriculture, horticulture, and public health everywhere?  Who will recognise when a local species that's a canary for water quality or temperature rise is replaced by a similar-looking exotic pest with a wider tolerance?  It's not only the world's climate that's close to crisis point.

After I wrote the bulk of this post, two very relevant articles were published.

One claims there are more taxonomists and fewer undescribed species than we have estimated.  This would be good news if future estimates reach the same conclusions, but it does contradict what has been termed elsewhere a mass extinction of taxonomists.  (I do note the authors include untrained taxonomists in their numbers; that's a different issue, but, briefly, if taxonomy is to be practiced as a science, it needs its practitioners to be trained in population genetics, evolution, statistics, comparative biology, and the scientific method, and working in institutions that can archive their specimens and records, and provide collections, lab, and library support.  Many biologists' low opinion of taxonomy leads them to the opinion that anyone can do it without training and a thorough background in relevant science.)

The other article analyses the citation problem, giving reasoned and evidence-based support for much of what I'm saying here.  (Commendably, for a paywalled journal, this opinion piece is freely available.)

So here's a challenge to other biologists: if you value the taxonomic system that enables you to describe and interpret your research, cite at least one taxonomic paper that underpins each paper you publish, and commit to never omitting any relevant ones.  It's a small thing to do to support the discipline that supports your work.

References not hyperlinked in the text.

Garnock Jones PJ, Webb CJ. 1996.  The requirement to cite authors of plant names in botanical journals. Taxon 45: 285-286.

Sykes, W. R.; Garnock Jones, P. J., 1979: A new combination in Syzygium for Eugenia maire (Myrtaceae) of New Zealand. Journal of the Arnold Arboretum 60: 396-401