Saturday, January 31, 2015

Are Linnean ranks and cladism incompatible? (That special issue)

(The following is the eighth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The next contribution is that of the late Richard Brummitt who died between the Melbourne symposium promoting paraphyletic taxa and the publication of the resulting special issue. The manuscript was apparently adopted from a talk he gave at the symposium.

Brummitt's death was a great loss to the botanical community; he was influential, knowledgeable and had friends across the entire planet. In the present context, I respect him as the only proponent of paraphyletic taxa whose argumentation ever made sense to me – if, that is, certain controversial assumptions are accepted. This may sound like faint praise, but it is more than can be said about many other arguments that are used in the discussion.

Brummitt was also certainly a good writer, as will be evident in what follows, but nonetheless I find myself unable to agree with his conclusions. I will go through the paper from the beginning until we hit the crux of his case.

Tuesday, January 27, 2015

Botany picture #191: Scleranthus biflorus

Apparently I cannot currently muster the energy to deal with the next paper from that special issue, so here is another picture from the recent field trip. Scleranthus biflorus (Caryophyllaceae), New South Wales, 2015. More weird than pretty, I'll admit. The spiky balls to the left and in the background are fruiting heads of Acaena novae-zeelandiae (Rosaceae).

Saturday, January 24, 2015

Au contraire

One of the things that has often struck me when contemplating religion is that I do not only disagree with several core claims made in its favour, but I feel that these claims are completely upside-down. In other words, not only are they wrong, but instead I feel that they are so much the opposite of what is really the case that one might start to suspect psychological projection to be at work.

I am not thinking of claims about actual evidence for the truth of religion - that is a different issue - but of second order claims about the benefits of religion. In particular, popular pronouncements along these lines:
  1. Life without god is totally pointless and meaningless; we need god and divine commands to give meaning to our lives.
  2. The conclusion that we are annihilated at death is depressing, and belief in an immortal soul, in our continued existence after death is much better.
  3. Atheists must be immoral because without gods and holy books they have nothing to base their morals on. Therefore, they should not be trusted.
One after the other...

Tuesday, January 20, 2015

Botany picture #190: Coreopsis lanceolata

One of the amazing things about daisies (Asteraceae) that is hidden to many non-botanists is how they do a lot of things with an inflorescence that other plants do with a solitary flower. To me this appears to be a clear case of convergent evolution: There is a limited number of good solutions to a given problem, and so evolution converges on them over and over again.

As background, most readers will know that what appears to be a daisy "flower" is really a head consisting of numerous small flowers called florets:

The small structures in the middle are the disc florets, some of them in bud, some of them open, and the latter each with five petals and a ring of fused stamens surrounding a forked style in the middle. But, unbelievable as it may sound, the large yellow pseudo-petals around the flower head are also individual flowers. They are called ray florets and are essentially an extreme version of a zygomorphic flower like those found in Goodenias or Lobelias, for example; in this case, the three petals forming the lower lip of the flower are massive enlarged while the two petals forming the upper lip are reduced. In many species they also have their own style (although no stamens), further demonstrating their true nature.

Now as I wrote above, daisy heads sometimes converge on the same functionality as individual flowers of other plant groups. The case I noticed recently is Coreopsis lanceolata. This species, introduced to Australia from North America, has differentiated bracts. The outermost "pretend" to be a calyx, so they have the same role as the outermost, small, green leaf organs of a regular solitary flower and, it has to be said, as the bracts of most other daisies: to protect the developing organ in bud.

However, in Coreopsis lanceolata there is also an inner group of bracts that are larger and less herbaceous, often already brownish when the head is in flower:

What those inner bracts are good for becomes apparent when the head has finished flowering. The petaloid ray florets fall off, each disc floret starts forming one one-seeded fruit, and at the same time the inner bracts close around the developing fruits to protect them:

When the fruits are fully developed, the inner bracts spread apart again to allow their release. In this way, these bracts behave pretty much like the carpels forming a capsule in many solitary flowers.

Don't know about you, but I find this pretty amazing.

Saturday, January 17, 2015

Botany picture #189: Senecio pinnatifolius

The past few days I was on a field trip to Kosciuszko National Park with one colleague and two students, and I came back totally tired. I think twelve years ago running around at ca. 2,000 metres above sea level was less exhausting for me.

I don't need to write much about the area because I already did so, after I undertook a similar field trip two years ago: first part, second part. So this time around let's simply combine a mountain landscape with a botany picture: Senecio pinnatifolius var. pleiocephalus (Asteraceae) on the way from Charlotte Pass to Blue Lake. Daisies are an extremely important part of the alpine flora of this country, perhaps even more so than on other continents.

Monday, January 12, 2015

Much ado about absent ancestors

(The following is the seventh part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Pages 79 to 88 of this special issue meant to promote the acceptance of supraspecific paraphyletic taxa in biological classifications are taken up by a contribution entitled Paraphyly and polyphyly in the worldwide tribe Rubieae (Rubiaceae): Challenges for generic delimitation. Written by Friedrich Ehrendorfer, Michael Barfuss and Vladimir Vladimirov, it is perhaps best described as a concise review article summarising the current state of knowledge about phylogenetic relationships in their group of interest, and as such I found it extremely interesting and rewarding to read.

Even if they are not familiar with the scientific name, most people in the northern hemisphere will know Rubieae. They are characteristic herbs with seemingly whorled leaves; only seemingly because in reality there are only two true leaves, and the additional members of each whorl are derived from stipules, as demonstrated by the fact that only up to two side branches arise from each node. The flowers of these plants are usually small, radiate and white or yellow. The group has an extremely wide distribution; there are even native representatives here in Australia.

The phylogenetic studies discussed in the paper show that the two largest genera that are traditionally accepted in the Rubieae, Galium and Asperula, are horribly non-monophyletic in their current circumscriptions. Faced with this situation and considering the context in which the paper has been published, one would now expect, or at least I would expect, that the authors argue for the continued acceptance of these genera as non-monophyletic. That was, after all, the whole point of the symposium in Vienna that inspired the special issue.

Friday, January 9, 2015

Comparison of phylogenetic tree viewing programs: TreeView, FigTree, Dendroscope

It seems as if I could productively conclude the theme of how to root phylogenetic trees by providing an overview of the tree viewers I have some experience with.

When you do a phylogenetic analysis in programs such as PAUP, TNT, RAxML, MrBayes or BEAST, you do get a phylogenetic tree, but it is not a graphic to look at. Instead, the standard format for phylogenetic trees is that of a text file in the Newick format, e.g. "(speciesA:4,(speciesB:6,(speciesC:2,speciesD:3)95:2)76:1)". The brackets show how the terminals of the tree are grouped, the numbers after the colons are branch lengths, and the other numbers following directly behind brackets are clade support values. All the information is there, but that is not a very clear way of displaying a tree, especially if it has dozens or hundreds of terminals.

The programs discussed below are used to display phylogenetic trees and to transform them into vector graphic files that can be used for the preparation of scientific publications.

The screen shots below show the same tree displayed in each program as a phylogram with clade support values.

Thursday, January 8, 2015

So how great is a god really that needs gunmen to do his work?

As always the following is my personal opinion and does not necessarily reflect that of my employer, line manager, family, friends, colleagues, computers or pot plants.

So about the terrorist attack on Charlie Hedbo...

I think the best way to react to somebody being murderously offended at the publication of satire is to repost some satire:

This is from Jesus and Mo, a wonderfully cheeky weekly comic strip, although admittedly the Mohammed character is said to be a body double.

To a certain degree I am trying to understand the logic of the murderers, although I am aware that one probably should not expect much logic. Reportedly, as they were massacring their victims, they shouted "we have avenged the prophet Mohammed" and "God is great". This raises the immediate question of why god, if he is indeed as great as they claim, cannot deal with blaspheming satirists himself, or in other words why exactly the murderers in cases like these think they need to commit such murders in god's name.

Surely if drawing a caricature of Mohammed is worthy of terrible punishment, god can just throw the artists into hell after they are dead? Or if he needs a speedier solution, maybe god can strike them with lightning? But of course that doesn't happen; why it is nearly as if god didn't actually exist! Perhaps the shouts of "god is great" primarily serve to reassure those who do the shouting, to drown out the little voice of doubt inside their heads; and to get rid of outside voices of doubt they use guns.

A blast from the past

A colleague found this when she tidied up her office. I am no spring chicken, but even when I was a student I never saw anything lower than PAUP version 4. Then again, I had a university course where we were shown how to use Hennig86, another phylogenetics software that I never had reason to use thereafter...

And of course I don't seem to have any computer with a floppy disc drive any more.

Wednesday, January 7, 2015

More on outgroup rooting: whither root branch length?

Continuing on the theme of rooting, there is a somewhat peculiar aspect to outgroup rooting. In the previous post, when I explained five different ways of rooting a phylogenetic tree, I used the following tree to illustrate outgroup rooting:

Species A is the outgroup to the ingroup BCDE. As we can see, the long red branch separating outgroup and ingroup has been assigned entirely to the stem of the ingroup, leaving the outgroup to sit on a zero length branch. There is, however, no logical reason why this has to be so. We could just as well divide the length of that branch evenly among ingroup and outgroup:

This is what the tree viewer software FigTree appears to do automatically when asked to outgroup-root an unrooted tree.

At the other extreme, we could also assign the entire length of the branch to the outgroup. This is what the tree viewer software TreeView does as a default:

It is important to keep in mind two things. First, although at first sight the above tree looks as if it has an unresolved polytomy at the base, where I placed the blue circle, the tree is still exactly the same as in the two previous images.

The confusion that some observers may experience when faced with such a tree arises from the unconscious assumption that the connection to the rest of the tree of life also goes through the blue circle, giving that node four connections. Seeing a lot of tree figures conditions us to expect that connection to go off from the vertical line. In reality, the rest of the tree of life connects somewhere along the red internode, and if we were to make the connection the red internode would be transformed into two horizontal lines and one vertical line. Consequently, the node in the blue circle actually has only three connections, the same number as every other fully resolved tree node: one from the ancestral lineage, two towards the descendent lineages.

The second thing to keep in mind is that the assignment of the length of the red branch is, under outgroup rooting and in the absence of additional information provided by a yet more distant outgroup, totally arbitrary. So no matter which of the above three ways of doing it you will find in a phylogenetic publication, they are all fully equivalent, even as the appearance of the trees is superficially different.

Monday, January 5, 2015

How to root a phylogenetic tree: outgroup, midpoint and other methods

Googling terms like "outgroup rooting" will, of course, provide several other places on the internet where people have explained how phylogenetic trees can be polarised, be it on university websites or on blogs of other phylogeneticists. Often, however, they seem to mention only the first two of the methods I will list below, and consequently it seems useful to add my take on it.

The problem is easily explained. All phylogenetic methods can produce a phylogenetic tree, that is a tree-graph showing the evolutionary relationships of its terminals, but many of them are silent on the  polarity of the tree. Thus for a study of the species A, B, C, D and E we may retrieve the following "unrooted" tree:

In this case, we know that A is very distant from the other four species, but we do not know in what direction evolution proceeded. It could be that A is the earliest diverging species, but it could also be C, for example, and the very long branch on which A is sitting is simply due to very fast change along that lineage.

As a different example closer to home, consider hominid evolution. Most people will know that the phylogeny of the great apes has been resolved as (orang-utan,(gorilla,(chimp,human))). But if we were ignorant of the root of the tree - here between organ-utan and the rest - it could just as well be (human,(chimp,(gorilla,orang-utan))).

So how do we know that the orang-utan is the earliest diverging great ape? How do we polarise, or "root", our ABCDE tree? There are several commonly used ways of doing this, and they each come with their own assumptions.

Friday, January 2, 2015

Believe me, you wouldn't want your five year old to breathe this either

Trick question: what is this haze covering our suburb?

(a) Fog.
(b) Chemical warfare.
(c) The toxic fumes resulting from a successful attempt to make it into the Guinness Book of World Records in the category of Pointless Waste of Perfectly Good Car Tyres and Petrol?

Hint: it smells like (b).

Thursday, January 1, 2015