New England holiday trip, part 1

We are making use of school holidays to go on a little trip to Australia's New England area, i.e. the north-east of New South Wales. This is the first time we visit it. We have been making our way there slowly over Saturday and Sunday, and on Sunday evening we were generously welcomed to Armidale by botany professor Jeremy Bruhl, his family, and fellow botanist Ian Telford. We will explore waterfalls, forests and lookouts of the New England high country over the next few days.

The above is the view from Moonbi Lookout back towards Tamworth, the last really large town we passed through before reaching Armidale (it is too far away to be visible though).

Today I dropped into the N.C.W. Beadle Herbarium of the University of New England, of which herbarium Jeremy Bruhl is the director. Read more about this scientific collection, its importance and history on its website.

An impressively floriferous and sweetly smelling shrub we saw on the way near Premer is this Santalaceae. I am reasonably sure it is Choretrum candollei.

The Templeton Test in parsimony analysis: part 2, how to do it in PAUP and TNT

After discussing the Templeton Test in an earlier post, this post is about how to conduct it in practice.

Floriade 2015

Impressions from our visit to the Floriade spring festival yesterday.

Tulip mania! Interestingly, the red ones were still behind the white and yellow ones, meaning that the plantings will only really come into their own in a week or so.

With the first World War a hundred years ago, Australia has had war related events since last year and is set to continue until 2018. As a German I find it fascinating to see the difference in perspective, as in Europe the horrors of WW2 have totally overshadowed anything that happened in the first, which is also much further back in the past. But Australia lost such a large number of young men that WW1 left a more lasting impression than it did in much of Europe.

Anyway, poppies are apparently associated with remembrance of war. Here people could pay a bit of money for a poppy to place on the wall, and the proceeds went to a charity.

The view from above - this is the first time I was on the Floriade's Ferris Wheel.

Lifeline Book Fair

Great haul at the LifeLine Book Fair this spring, it was a good idea to go early on Saturday this time.

The Templeton Test in parsimony analysis: part 1, principles

When we want to know whether a taxon, for example a genus, is monophyletic (and thus acceptable in a phylogenetic classification), the first thing to do is to infer a phylogeny. We may then find a topology like the following:

Genus A is non-monophyletic on this tree because B is sister to A2. However, the support value for clade A2 + B (the red number, 63 of 100) is not exactly stunning; if this is Bayesian Posterior Probability, you would want 95 or higher, and if it is bootstrap or jackknife you would still want to see at least 80 or so, preferably more. With so little support it could just as well be that these relationships are wrong and genus A is monophyletic after all.

(It is amazing, by the way, how many people find it hard to intuit that when discussing the status of A the red support value is indeed the relevant one. If it is high then precisely that number provides support for the non-monophyly of A while the black value is irrelevant - it merely shows that A1, A2 and B belong together but doesn't tell us anything about A versus B. Some time ago I even had a peer reviewer who got that wrong at first. Perhaps people are just so trained to look for how strong the evidence for monophyly is that they can get confused when they need to look for evidence for non-monophyly.)

So yes, the tree shows A as non-monophyletic, but we can't be sure if the evidence is strong enough. Is there another way of testing whether, let us say, A is "significantly" non-monophyletic?

This is where, for parsimony analysis, the Templeton Test comes in, which by the way doesn't have anything to do with the Templeton Foundation.

Botany picture #214: Grevillea arenaria

Grevillea arenaria (Proteaceae) is described in the online flora of New South Wales as "red, pink or orange, often green or yellow at base", but if the label on this specimen in the Australian National Botanic Gardens is correct then it is surely quite on the green side. Perhaps a variant? Certainly the most unusual flower colour I have seen in this genus so far.

Isaac Asimov's Foundation

I spent much of the week at a meeting in Tasmania. On the last day I had time to browse a book store and finally bought the first Foundation novel after I had only found sequels and prequels at the local book fair so far.

It is not so much a novel as a compendium of several shorter stories, each with their own characters and representing several stages of the development of the eponymous Foundation. I have written before about some of the other books in the series (Foundation and Empire, Foundation's Edge). Although my observations on this book are similar to those on the later ones, somehow it doesn't feel quite as blatant.

Botany picture #213: leafy liverwort sporophyte

Recently went through a couple of old pictures and found this very lucky photograph. It is already a bit lucky to find liverwort sporophytes because in contrast to those of mosses and hornworts they are very soft-bodied and short-lived. And then I was lucky enough to get quite a decent snapshot despite limited light in the understorey and the notorious problems my camera has with focusing on thin objects.

I do not know the species or even the genus, but it is a leafy liverwort growing on a log in a southern New South Wales national park in 2012, and it shows some of the typical traits of a liverwort sporophyte: soft stalk, sporangium (~capsule) opening with four valves, and the longish elaters in the sporangium that help disperse the spores with their hygroscopic movement.

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.