Botany picture #178: Dianella

Today was a public holiday, and we met with some people to go for a walk in Mt Majura Nature Reserve. Among the spring flowers out was this Dianella (Phormiaceae); note the curly filaments and the morphological differentiation of apical and basal parts of the anthers. Unfortunately, figuring out what species it is seems to be rather hard in this genus...

Botany picture #177: Klasea nudicaulis

Yesterday I finally received the specimens from my collecting in Europe earlier this year and started putting names on the so far unidentified specimens. The above species turned out to be among them: Klasea nudicaulis (a.k.a. Serratula nudicaulis, Asteraceae).

I can't help myself but the generic circumscriptions in the thistle tribe Cardueae don't really seem intuitive to me. I look at something like this and go, oh, obviously a Centaurea, and half the time it turns out to be something else, and I have no idea why. The characters used to differentiate the various genera in the keys are usually those that I would expect to be rather homoplasious, like the shape of the end of the involucral bracts.

Still don't understand what supernatural means

Some time ago I wrote that I don't really understand what supernatural is supposed to mean. Recently I took the opportunity of a discussion on whether humanism should or should not include a commitment to naturalism to pitch the question of what the opposite - supernaturalism - would entail. Although a few answers were helpfully provided, I sadly find none of them very useful.

Basically, I have the suspicion that although the word is continually used in rather important claims, such as that science has nothing to say about the supernatural, or that, see above discussion, one should not carelessly dismiss the supernatural, nobody actually has a clear definition of the concept supernatural.

Of course, a lot of people have examples that pop into their heads when they hear that word, and they would be tempted to reply with "something like demons and telekinesis". But that is not actually a definition, and my question is one step further back. Why would it be considered to be useful to call demons and telekinesis supernatural as opposed to natural? What is the difference between demons and horses, or between telekinesis and gravity, that would make it meaningful to call the first in these pairs supernatural and the second natural and, and this is where the important consequences come in, justify the conclusion that they are consequently beyond the scope of science?

To see what I am getting at, imagine that there is a thing or process called Ulkjam. You have never heard of it before, but I know all about it except whether it should be classified as natural or supernatural; that is what I want to know from you. You can ask me about all of its characteristics and attributes, and I will be able to answer. So what would your question(s) be to help you figure out as quickly and decisively as possible whether Ulkjam is supernatural or not?

So far, nothing useful has come up:

Botany picture #176: Romulea rosea

Some of the lawns in our suburb would look quite familiar to South Africans, I suspect, because there is an astonishing number of introduced plants from the Cape Region growing in them. In addition to the ubiquitous cape weed, which is really doing well for itself this year, there is also this little pink liliaceous monocot called Romulea rosea (Iridaceae). With its tiny size it seems harmless enough at first sight but it is apparently a declared noxious weed.

Another remarkable thing about it is the silliness of its common name: onion grass. Neither an onion nor a grass, this plant is thus a testament to the lack of imagination of its namers.

Botany picture #175: Daviesia genistifolia

One of many local pea-flowered Fabaceae, this Daviesia genistifolia we recently saw at Mulligan's Flat Nature Reserve is not the kind of plant you want to accidentally fall into. The spines are quite unpleasant.

Phylogenetic trees in a matrix format in R

Yesterday, today and tomorrow I am participating in a workshop called 'Computational Macroevolution' run by Dan Rabosky, one of the leading experts in evolutionary modelling. Today we are learning about modelling changes in diversification rates, but yesterday he did a more general introduction into handling phylogenetic trees in R, especially with the APE package.

This was really useful because so far I have used R only for general statistics or plotting, never for dealing with trees. Among other things, it is interesting to see how R actually saves trees. It works like this:

In R, a phylogenetic tree is a list of four types of data.

The first is called Nnodes and is simply the number of internal nodes that the tree has. In a fully resolved tree, this should be number of terminals minus one.

Unsurprisingly, there is also a vector of terminal names.

The third element of the list are the internodes. They are organised as a vector of pairs of node numbers, where the first is always the parent node and the second is the daughter node. So a tree like ((A,B),(C,D)) would be structured as follows:

5 - 6
5 - 7
6 - 1
6 - 2
7 - 3
7 - 4

If there are N terminals, then nodes 1-N are the terminals themselves, obviously in the same order as in the vector of terminal names. Node number N+1 is always the root node, the others follow by order of distance from the root although really that is an arbitrary convention.

It is also obvious that a fully resolved and rooted tree will have two entries in the vector of internodes for every internal node. If there are polytomies then there are more than twice as many internodes as internal nodes, and there are less than N-1 internal nodes.

Finally, there is a fourth element of a phylogenetic tree, the vector of branch lengths (if any). The order is the same as in the vector of internodes.

I don't know exactly how an unrooted tree is handled but that will be easy to figure out. Anyway, useful stuff.

Botany picture #174: Banksia serrata cone

A cone of Banksia serrata (Proteaceae), Australia, 2014. Often, seemingly simple and everyday things can lead to a number of intriguing questions when thought through. In this case, note first that there are very few follicles ("seed pods" - the red, hairy blobs in the picture) developing from what was a spike of dozens if not hundreds of flowers. In other words, most flowers were unsuccessful.

But why? Are these plants suffering from pollinator limitation, that is do they not get enough pollen to fertilise more flowers? Or do they get enough pollen, but most of it is from incompatible individuals? Many plants have incompatibility systems to ensure that they only accept pollen from sufficiently distantly related individuals, to avoid inbreeding. Maybe there just aren't enough compatible sex partners within a realistic distance, perhaps because the local population is genetically impoverished? Then again, maybe the plant could theoretically develop more genetically worthwhile fruits but it only ever "wants" to develop a few per cone because it cannot afford more, resource-wise, and so it aborts the rest. Offspring is expensive, and Proteaceae generally live on very nutrient-deficient soils.

Whatever it is, there is an interesting question here. I assume people will have studied it already, but I just don't know at the moment.

Another one is raised by the dry, dead flowers still attached to the cone. Some Banksias drop the dead flowers, e.g. B. integrifolia, some keep them. The latter state is often interpreted as an adaptation to frequent fire, but I recently heard an ecologist argue that many of the characters traditionally interpreted in that way arose before Australia dried out and became very fire-prone, so they couldn't have been adaptations. Well... don't characters always have to arise randomly before selection can begin to work on them? Where would you draw the line then?

That's the nice thing about the world around us: there is so much to figure out.