Why didn't I publish this? Quasi-Repost: Messing around with trees: Ardipithecus ramidus

Hey there, haven't posted anything in a while haven't I? Well this isn't a new post either. I just went through some of my older stuff and stumbled upon this Post I wrote a year ago, which I never published. Probably because I thought it's bad. Well, either I've lost my sense for quality, or I didn't realised this Post was actually quite interesting. Be it as it may, here it is:

A few weeks back when I desperately sought for stuff to waste my time with, I came up with a very nice, but also quite strange Idea: How about ruining some phylogenetic trees?

There are some nice Tools on the Internet which enable you to execute small to middle scale analyses for free and without relying on huge clunky programs. One of them, which I use quite a lot right now, is on the homepage phylogeny.fr (Dereeoer et al. 2008). It’s usually a tool for DNA data, but with some little adjustments you can also use it for basic morphological Datasets.

For my first target, I decided to attack a big fish and therefore the most easiest to attack: Ardipithecus ramidus.

The authors didn’t publish a tree by themselves, but they did publish a nice little table of characters to show how and  good ol’ Ardi is related to other hominids.

White et al. 2009

So my first step was to reconstruct a tree from this table, the results weren’t really surprising:

Now what happens if I change some of the more controversial characters (some characters of the pelvis and some regarding the C/P3 complex) from “derived” to “ancestral” (I refuse to use the word “primitive” in this context)?

Well looks like this didn’t do the trick. Let’s try something more drastic, like deleting all dental characters.

Gotcha!

You see, from the 68 characters that were listed in the initial character table, 34 of them were located on the teeth. And most of the phylogenetic signal which separated Ardi from the other early hominids is located within those 34 characters.

I would’ve loved to deconstruct this tree even further, but I couldn’t find any means without doing completely ridiculous stuff. This is mostly because of the way White et al. (2009) defined their Outgroup Taxa. The Outgroup is one of the most crucial parts in phylogenetic reconstruction because it defines the ancestral state of all characters. Therefore different Outgroups can change the topology of your tree in a huge way. The Outgroup characters in the Table from White et al. consist of inferred character states from a hypothetical last common ancestor. Since we have hardly an Idea how this last common ancestor looked like (I wrote something about this here), there is a huge space for “inference”, others might even call it “speculation” or “guessing”.

Keep in mind that this whole stuff is just the result of me, messing around with this stuff. Nothing of this has any scientific value. However, I still learned some interesting stuff while doing this.

First of all, although discussions about Systematics and phylogenetic trees can become really boring from time to time, they’re sometimes very helpful when you try to get to the core of a certain problem. They also provide nice means to visualise these problems and the effect it has when you change certain parameters.

In the end, when you intend to challenge the initial taxonomic placement of Ardipithecus ramidus there are two things you have to look at.

Try to show that most of the dental characters White et al. (2009) used are redundant and/or false and try to show that their inferred ancestral character states are wrong.

You see, Phylogenetic trees can be good for something and if it only is for stating the obvious...

References:

Dereeper A. et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist Nucleic Acids Research. 1; 36

White, T. D. et al. (2009) Ardipithecus ramidus and the Paleobiology of Early Hominids. Science 326, 64. S 64-86.

Some thoughts on the phylogenetic relationships between great apes and humans (and why morphology fails to answer this question)

Taxonomy isn’t a really satisfying branch of evolutionary biology, especially if you’re interested in the phylogenetic relationships between great apes, hominins and humans. You always tend to step on someone else’s toes and sooner or later this other person starts to harass you with critique. One of the standard arguments which are brought up against almost any kind of phylogenetic study is that the characters you used for your phylogenetic reconstruction are misleading, because they’re homoplasies. “Homoplasies” are characters which evolved independently in two closely related species and are usually your biggest enemy when it comes to taxonomic questions. 

fig. 1 Today's topic: The "correct" phylogenetic relationships between great apes and humans and why morphologic characters fail to reproduce these results.

This problem seems to be overabundant in Paleoanthropology, since I have yet to see a single taxonomic paper which isn’t immediately criticized for using homoplasious characters for their hypothesises. This is probably due to the reason that morphological characters in general are having a hard time reconstructing the “correct” phylogenetic relationships between great apes and humans (fig.1), which was established with molecular characters (e.g. Wood & Collard, 2002; Wood & Harrison, 2010; Strait & Grine, 2004). And if your characters aren’t able to reproduce the correct phylogeny between extant species, how can you expect them to get it right with fossil species?

Recently one of my Professors pointed me towards an interesting problem which made me wonder if those difficulties are really due to too many homplasious characters in your datasets.

Imagine a Population “P”

This Population has some characters which are polymorphic, which means that they exist in different states within this population. For the sake of simplicity I will only use two characters. The first character has either the state “+” or “-“

The second character has either the state “circle” or “square” (I’m too inept to put those symbols within this text –sorry).

Now this Population starts to split up.

Shortly after P1 split up from P, the rest of the original population splits into two additional subpopulations (P2 & P3).

Eventually all those three subpopulations will evolve into three different species

If we look at the pattern in which those Populations split from each other, we can see that P2 and P3 are closer related, because they got separated after P1 split away.

Now imagine that we weren’t able to witness this pattern and instead we have to reconstruct it with a cladistic analysis, which is usually the case if you want to know how extant species are related to each other. The problem here is that there is no clear signal. Instead your results depend highly on the character you’re using. Here we are in a situation where we have three equivocal hypothesises just because you had an polymorphic, ancestral population which split up so fast, that it wasn’t possible to fixate one character state within the whole population. Instead the ancestral polymorphic state was carried into those new subpopulations and the trouble we encounter if we want to use those characters for phylogenetic reconstruction is simply because of this incomplete lineage sorting and not because the character were homoplasious.

Of course I came up with this example, because we can see the exact same phenomenon if we look at molecular studies which dealt with the phylogenetic relationships between great apes and humans. Satta et al. (2000) found that out of 46 genetic markers, only 60% supported the “true” phylogeny (see fig. 1), the other 40% either supported a Human-Gorilla dichotomy, a Gorilla-Chimpanzee dichotomy, or a trichotomy.

Salen et al. (2003) came to similar result as they used “Alu-SINEs” to reconstruct the great ape phylogeny. Although Alu-SINEs are probably the best characters you can use to resolve any kind of phylogenetic relationship within primates, simply because it’s highly unlikely that they independently occurred at the same place on the DNA. Nevertheless they found one Alu SINE which humans and Gorillas had, but Chimpanzees didn’t.

But how polymorphic was the ancestral population of Gorillas, Chimpanzees and Humans on a phenotypic level?

This question is almost impossible to answer, at least for now. we have no Idea how the genotype relates to the phenotype as long as we aren’t able to close this gap we’re not able to make anything more than vague assumptions about this question. Looking at this whole story of Neanderthals and “Denisovans” interbreeding with modern humans (Greene et al., 2010; reich et al., 2010), which probably means that we have to broaden up our own species to include at least the Neanderthals if not even Homo heidelbergensis, I think we can see that a species can vary pretty much on a phenotypic level without interfering with reproduction.

This whole story definitely doesn’t make things easier since we now have two problems: Convergent evolution and incomplete lineage sorting. But I think we can at least try to differentiate things a little bit more. Although we have no Idea how much incomplete lineage sorting has affected the phenotype of the African great apes and humans we can’t rule out that it had no effect at all. Therefore it’s pretty much futile to make any assumptions about the “quality” of certain characters, since we have no idea to what extent those characters were affected by incomplete lineage sorting. As we could see, characters can be pretty much invulnerable to parallel evolution and still indicate wrong phylogenetic relationships (Salen et al. 2003).

Maybe we should instead explicitly look at each and every character, especially those which support the “correct” tree and test, if they share a common origin.

References:

Collard M, & Wood B (2000). How reliable are human phylogenetic hypotheses? Proceedings of the National Academy of Sciences of the United States of America, 97 (9), 5003-6 PMID: 10781112

Green, R.,et al (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021

Reich, D., et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature, 468 (7327), 1053-1060 DOI: 10.1038/nature09710

Salem, A. (2003). Alu elements and hominid phylogenetics Proceedings of the National Academy of Sciences, 100 (22), 12787-12791 DOI: 10.1073/pnas.2133766100

Satta Y, Klein J, Takahata N (2000). DNA archives and our nearest relative: the trichotomy problem revisited. Molecular phylogenetics and evolution, 14 (2), 259-75 PMID: 10679159

Strait DS, Grine FE (2004). Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa. Journal of human evolution, 47 (6), 399-452 PMID: 15566946

Wood, B., Harrison, T. (2011). The evolutionary context of the first hominins Nature, 470 (7334), 347-352 DOI: 10.1038/nature09709




P.S.: I just realised that used almost the exact same formulation for the title of this Post as I used for my last title. I'm deeply sorry for my lack of creativity. (11.10.2011)

Speculation on Speciation

There is one topic which somehow touches almost every major debate in Paleoanthroplogy and this is the question about how speciation actually works. There were a lot of very smart people, who already wrote about this stuff, and I even read some of them. But a large proportion of what I’m going to say about this topic comes from my own thoughts on this topic. So if someone finds a mistake in my arguments, please let me know.


When it comes to speciation, there are basically two different opinions on how speciation could work. The first one is sometimes called “punctualistic” or “phylogenetic” and says that speciation usually results in a split in which the ancestral species splits into two different “offspring-species” (there is probably a more suitable term for it, I just can’t remember the English translation).

The second one is called “gradualistic” or “anagenetic” speciation and says that one species can, if there is enough time; evolve into another species without any form of splitting.

Now although there are many species concepts out there, the main criterion to recognize a species is, if their members are able to interbreed with other animals. This means that no matter what type of speciation process we propose, at some point during this process there has to be some kind of “breeding barrier” (once again, I’ve no Idea how to translate this term), be it either geografical, behavioural or otherwise.


Now let’s take a look on how this stuff actually works in case of a punctualistic speciation:

Exdample for a punctualistic speciation: Assume a Species "A" lives in a certain habitat "X". Now due to some reasons (e.g. a geological event), a barrier arises in said habitat. This barrier changes the enviroment on both of its sides and furthermore prevents the now separated populations of "A" to exchange their genes. With time, those two sperate populations will adapt to their new enviroments and will become two distinct species.

Ok, this was quite easy wasn't it? But how about gradualistic speciation? Her I'll have to admit that although I spent quite some time on this question, I just could come up with one scenario:

1. Let’s assume the species we’re looking at is restricted to one habitat

2. Let us further assume that all population of said species are able to exchange there genes with on another.

3. Now the habitat of said species changes and due to the wonder of natural selection the species adapts to those changes.

4. As time goes by the species within that habitat would differ significantly from the species we had before this process started, so that we could safely say that we have discovered a new species.

There is only one big problem with this model. If we assume a constant gene flow between the seperate populations of our example species, than this means that there never was any kind of mating barrier at any point in time. So how can we be sure that the species we witnessed at the end of that process isn’t able to interbreed with the species we observed before this whole thing started? Sure, we could assume that since both “forms”, as I might call them right now, are so different that they probably wouldn’t have interbred, if they would’ve lived at the same time.
This assumption is pretty similiar to the concept of a “Chrono-species” which defines species solely after their chronological appearances in the fossil record.
The Problem here is that we’re not able to test, whether or not, those species really weren’t able to interbreed. It is as always when we have to deal with extinct species, we simply can’t be sure about it. In the end the only safe thing we can say is that every model on the evolution of a certain species, which relies on a gradualistic model of speciation, is highly speculative.


There are two recent examples within Paleoanthropology where this Problem occurs. The first one is the possibility to draw a direct line from Australopithecus anamensis to Australopithecus afarensis (Kimbel et al. 2006, Haile-Selassie et al. 2010). The other one are the genetical evidences of interbreeding between modern Humans and Neandertals (Green et al. 2010) and modern Humans and those strange people from the Denisova Cave (Reich et al. 2010).
In both cases we have clues, if not even hard evidence in the second example, of constant gene flow between several populations over a long period of time.

The interesting question now, is what we should do with these findings. Should we just keep these different species and use some kind of dodgy chrono-species concept or should we lump all those different species into one or probably two?

I have to admit that, due to my education, I am a little bit biased towards the “lumping” part.

Right now I am not convinced that gradualistic speciation is possible, or to be more precise, that it is detectable by us. So the scientifically safer way for us right now, is to stay cleer of this concept unless we can find some way to test it.

Surely, the last word isn’t spoken on this one, and right now a can think of several flaws in my own argumentation, but I’m still convinced that it is the preferable way of thinking.


References:

Kimbel, W., et al. (2006). Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record Journal of Human Evolution, 51 (2), 134-152 DOI: 10.1016/j.jhevol.2006.02.003
Green, R., et al. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021
Haile-Selassie, Y., et al. (2009). New hominid fossils from Woranso-Mille (Central Afar, Ethiopia) and taxonomy of early Australopithecus American Journal of Physical Anthropology DOI: 10.1002/ajpa.21159
Reich D., et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161

Just a mere thought: The upper limb of Apes and parallel Evolution of bipedalism.

Last week I wrote the following sentence:


” I have the impression that as soon as you find a fossil ape that probably walked on two legs, its being put into the human lineage without asking further questions about its true relationships.”

I think this needs some further explanation:
One of the key features for the classification of hominins is bipedalism, simply because we are bipedal. But are those very early, probably bipedal, fossil Apes really hominins? There are some arguments which reject theses hypothesises. Molecular genetics nowadays put the divergence between Chimpanzees and humans somewhere between 4 and 5 million years. Most of the fossils (Sahelanthropus tchadensis, Orrorin tugenensis and at least Ardipithecus kadabba) are older than this date. There are strong reasons to suggest, that you cannot move the date of divergence very far into the past. For more information on this issue I suggest reading John Hawks Post "Reviewing the clock and phylogenomics".  Also some traits which were used to classify those fossils as hominids are far from being unequivocal, as you can see at the discussion of Ardipithecus ramidus last week.
Ok, let’s assume that all those early hominins in fact are not hominins. They still show some traits that could be related to bipedalism aren' they? How can we explain that? The answer could be that bipedalism evolved more than once.


Is there any evidence for the convergent evolution of bipedalism?
Well, there is no direct evidence, but here I will present you a hypothesis where parallel evolution of bipedalism could be possible.
Reynolds (1985) showed that Apes in general (some in a larger degree than others) try to put more weight on their hind limbs. The main reason for this seems to lay in the more laterally oriented glenoid fossa of recent Apes. The lateral orientation of the glenoid fossa results in more flexible upper limb and enables suspensory Locomotion while in trees (Aiello, Dean, 1990). On the other Hand it generates higher stress on the shoulder-joint while terrestrial locomotion. This problem could be one of the reasons for the evolution of knuckle walking in Gorillas and Chimpanzees.
Now there is some evidence which points to the possibility that knuckle walking in Chimpanzees and Gorillas evolved twice (Kivell, Schmitt, 2009; Wunderlich, Jungers, 2009; Lovejoy et al., 2009), which means that hominid bipedalism didn’t evolved from a knuckle walking ancestor. What does that mean for the evolution of bipedalism?


Let’s assume we have a more generalized, not fully suspensory Miocene Ape with a flexible shoulder. Let’s assume further that this Ape has to climb down from his tree. Because the lack of strong flexors in the Forearm, he isn’t able to do efficient knuckle walking and his flexible shoulder makes it impossible to walk in a “normal” quadrupedal gait. The consequence would be that this Ape completely avoids walking on his upper limbs and instead will start walking bipedally. Looking at Ardipithecus ramidus this scenario seems not that unlikely. According to the Authors, Ardi was an above-Branch Quadruped while in the trees. On the other Hand, she had a flexible shoulder, at least of what could be told from the remains.


Under the light of this model, the evolution of traits related to bipedalism would be the logical consequence of the functional morphology of said Ape. This means, that if you put similiar selection pressures on different populations of this hypothetical Ape, it would result in the parallel evolution of bipedalism in these populations.


Well okay, everything I said above is more or less hypothetical, but what could be done to put it on a more solid ground?
Well momentarily I can think of two things: First you have to look how Apes exactly stress their forelimbs during terrestrial locomotion, there is some research done with it, but for what I know is that it’s not enough.
Secondly I think one should try to simulate this above mentioned “hypothetical Ape” and look what kind traits it needs to have that bipedalism is the most efficient option for terrestrial locomotion. With this set of traits you can start looking at the fossil record and try to falsify this hypothesis. The last thing is, in my opinion, the most important one, because not many models in human evolution are directly falsifiable through the fossil record.


I’ve been working on this thing for several months but two weeks ago I’m stuck. So I thought the best Idea would be to tell this stuff to a wider audience, which I have done now.
What do you think of it? Is it rubbish? Is it some old Idea which has been given up long time ago and I simply didn’t realized it yet? And if not, what else could be done to build it up to a real model and not some simple thought-experiment by an undergraduate student who has way to much time.


So, if you have any suggestions, please tell me. You will help me a big deal with it.

P.S.: If anyone got accsess to the "Journal of Zoology"  and could mail me the following article (Email: edgarneubauer[at]gmx.de), I would be very, very happy:

Larson, S. G., Stern, J. T. (2009). EMG of chimpanzee shoulder muscles during knuckle-walking: problems of terrestrial locomotion in a suspensory adapted primate. Journal of Zoology, 212 (4). S. 629-655.


References:

Aiello L., Dean, C. (1990) An Introduction to Human Evolutionary Anatomy. Elsevier Academic Press, London.

Kivell, T., Schmitt, D. (2009). Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor Proceedings of the National Academy of Sciences, 106 (34), 14241-14246 DOI: 10.1073/pnas.0901280106

Lovejoy, C., Simpson, S., White, T., Asfaw, B., Suwa, G. (2009). Careful Climbing in the Miocene: The Forelimbs of Ardipithecus ramidus and Humans Are Primitive Science, 326 (5949), 70-70 DOI: 10.1126/science.1175827
Reynolds, T. (1985). Stresses on the limbs of quadrupedal primates American Journal of Physical Anthropology, 67 (4), 351-362 DOI: 10.1002/ajpa.1330670407
Wunderlich, R., Jungers, W. (2009). Manual digital pressures during knuckle-walking in chimpanzees American Journal of Physical Anthropology, 139 (3), 394-403 DOI: 10.1002/ajpa.20994