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.
The blog of a systematic botanist of German origin, now working in Australia. It covers botany, phylogenetics, cladistics, science in general, freethought, and occasionally sillier issues.
Friday, January 9, 2015
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.
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.
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.
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).
(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
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