Vertebratist bias in action

The 72 last silhouettes submitted to PhyloPic as of today ca. 11am Canberra time break down into (not necessarily monophyletic) groups as follows:

11 non-avian dinosaurs
1 bird
7 primates
28 other mammals
1 reptile
3 fish
8 arthropods
8 land plants (all submitted by me)
1 kelp
4 other organisms

These are known species numbers for the various groups:

>1,000 non-avian dinosaurs known from fossils
ca. 10,000 birds
ca. 450 primates
ca. 5,000 other mammals
ca. 10,000 reptiles
ca. 33,000 fish
>1,000,000 arthropods (presumably a vast under-estimate)
>300,000 land plants
ca. 1,800 brown algae kelp species?
Other groups not mentioned here would include >25,000 nematodes alone, with 1,000,000 species estimated to exist, and of course molluscs, diatoms, bacteria and so much more.

In other words, even leaving aside the 'other organisms', relative to their species number birds are over-represented by a factor of four among recent submissions, non-avian dinosaurs by a factor of 220, primates by a factor of 320. Unsurprisingly then, arthropods and plants are vastly under-represented. And of course the database was already full of monkey and dinosaur silhouettes before those last 72 submissions.

This is par for the course; the same kind of bias is why you can get a Nature paper for discovering a new species of dinosaur or sufficiently cuddly mammal but not for discovering a new species of sedges.

Still, do contributors assume that bryologists and nematologists will never need to illustrate a phylogenetic tree figure? Just wondering.

No citation impediment in taxonomy?

(Two little edits made 5 Sept 2015.)

Recently a colleague placed on our tea room table a copy of Steiner et al, A Falsification of the Citation Impediment in the Taxonomic Literature, available in advance access in the journal Systematic Biology.

I am among those who believe that yes, there is a citation impediment in taxonomy, so this is interesting. Unfortunately, I am not entirely convinced that this study shows what the title claims it shows, or at least that it addresses the real issues.

As mentioned, the title of the paper states that the citation impediment has been "falsified". However, this is a complex issue. The authors themselves summarise the claims in question as follows:

The art of PhyloPic

As discussed in the last post, the idea behind PhyloPic is to provide "silhouette images of organisms", in other words just the black outline of the organism. That works well if you want to illustrate a phylogeny of insects, dinosaurs or mammals, because these taxa have very distinctive overall body shapes. It does not work quite as well if you want to illustrate a phylogeny of flowering plants, unicellular algae, or worms, for example.

There are two distinct problems. The first is that the truly relevant differences between organisms may be in their individual organs like flowers, leaf shapes, fruits, or mouth parts, for example, as opposed to the whole body. So to be useful, a collection of silhouettes should include individual parts of the organisms in question.

Second, a silhouette of an intricate organ like, say, a flower, may miss all relevant structure. Take this one, for example. When I first saw it as a small icon, I vaguely thought it might be a marchantoid liverwort, or maybe a particularly complex plankton species. It would not have occurred to me that it is a Hibbertia flower until I looked at the taxon name it was associated with. No, in a case like this it would really be good to see stamens and style, or to have gaps between petals and sepals.

Consequently, to maximise the utility of such an image collection across diverse groups of organisms, one would hope the definition of silhouette could be relaxed to include artwork with a bit more structure.

And apparently the PhyloPic collection is already somewhat flexible. In addition to silhouettes in the stricter sense, there are at least two other types of images in the database, although admittedly they are rare: Silhouettes that employ black and grey elements as in these recently submitted insects, and black silhouettes that also allow for white elements to visualise structural complexity as here.

For purely aesthetic reasons, I would prefer the latter. Obviously they also require some thought and talent. They would have to avoid lines that are too thin so that they still look good when scaled down. But the mayor challenge is simply to capture, using only black and white areas or perhaps only black areas with white gaps between them, the characteristics of a flower or fruit so well that (a) people will recognise the organism, (b) everything is morphologically correct, and (c) the result is attractive.

Scientifically correct botanical clip art could actually be something like a very special art form - just like of course new forms of visualisation, each with unique constraints, have always inspired botanical art.

PhyloPic

A few weeks ago we discussed a paper in our journal club that used dinosaur silhouettes in its figures and referenced PhyloPic as the source. So today I finally decided to check the website out.

PhyloPic is a repository of black/white silhouettes of organisms across the tree of life. The idea is that everybody can sign up and submit their artwork under some kind of creative commons or public domain license, and everybody can use the silhouettes to do just what the authors in the aforementioned paper did: decorate phylogenetic tree figures in publications or talk slides, educate, etc.

The idea sounds great, so I played around a bit today to see how well it works. The experience was, alas, a bit mixed.

Comment moderation on

Some spam bot seems to have discovered this blog, and it is getting annoying. Consequently I have just turned comment moderation on. I don't think it will make a lot of difference to readers of this blog. Discussions or questions happen, but they are rare.

Most people seem to find my blog when googling for one of the topics I have covered, especially phylogenetic systematics, the aromatic plant genus Minthostachys, the various posts on how to use this or that software tool or method, and, somewhat more to my surprise, three very specific posts on acknowledging peer reviewers, ResearchGate, and bracketed versus indented keys.

And that was always the idea: I don't expect to host any long discussions about paraphyletic taxa here, but maybe somebody will find some of my perspectives, information and how-to's useful. Comment moderation won't interfere with that, but it will make sure all those gibberish comments ending with links to health supplement sellers won't get through, and that's a plus.

Botany picture #212: Pachystachys spicata

At the moment I can't find the energy to write anything substantial, but I can just fill the blog with plant pictures that I have taken over the years. Here is another pretty Acanthaceae - a family that I have quite a lot of photographs of. Pachystachys spicata, originally from northern Bolivia, but in this case photographed at the Botanic Garden of Goettingen University. It is a weak-stemmed, scraggly shrub, and the flowers are obviously meant for hummingbird pollination.

Yellow-white Pachystachys lutea is more widely known and more often seen in botanic gardens, but I like the above species better.

Andere Laender, andere Sitten

One thing that gave me a bit of a culture shock after coming to Australia was the way in which plant taxonomists work here compared to how I had been trained by European and North and South American taxonomists.